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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtttgtttcttatggcagggccttctattggtctatcagttttgctctgtttcaaaattttgaactgtttaattattatttgtacagGCTGGTCAGTTGCATCTTGTGAAACCATACATGGTTGCAGTTCAGAGCAACAATGTCTCTGCTGTGAATGAAGCTTTGAATGAGCTTTATGTTGAAGAGG

Basic information

species Oryza sativa
transcript LOC_Os11g01380.1
intron # 25
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os11g01380.1 (Oryza sativa), 3'ss of exon 25
lower sequence: GRMZM2G057576_T01 (Zea mays), 3'ss of exon 24
--------------gtttgtttcttatggcagggc-cttctattggtctatcagttttg-ctctgtttcaaaattttgaactgtttaattattatttgtacagGCTGGTCAGTTGCATCTTGTGAAACCATACATGGTTGCAGTTCAGAGCAACAATGTCTCTGCTGTGAATGAAGCTTTGAATGAGCTTTATGTTGAAGAGG
              |    | | ||   |||| || |||  | | |     | ||||    || ||  ||||| | |||    | |  ||  | |||| ||||||||||||||||||||||||||||||||| ||||||||||||||||| |||||||| ||||| ||||||||||| ||||||||||||||||| |||||||
gttagcatctgattgaaaatctattcctgcagtgcactttgaatagaagccctgtttcaattccgtcccaaaaatctga---ttcttgttgctctttggacagGCTGGTCAGTTGCATCTTGTGAAACCATATATGGTTGCAGTTCAGAGTAACAATGTATCTGCCGTGAATGAAGCCTTGAATGAGCTTTATGTCGAAGAGG

upper sequence: LOC_Os11g01380.1 (Oryza sativa), 3'ss of exon 25
lower sequence: GRMZM2G115138_T01 (Zea mays), 3'ss of exon 9
gtttgtttcttatggcagggccttctattggtctatcagttttgctctgtttcaaaattttgaactgtttaattattatttgtacagGCTGGTCAGTTGCATCTTGTGAAACCATACATGGTTGCAGTTCAGAGCAACAATGTCTCTGCTGTGAATGAAGCTTTGAATGAGCTTTATGTTGAAGAGG
            | |  |  | ||  || |       | ||    ||  |  ||||| | |||    | |  ||  | |||| ||||||||||||||||||||||||||||||||| ||||||||||||||||| ||||||||||||||  |||||||||| |||||||| |||||||| ||||| |
-----------gtagt-gcactttgaatagaagccctatttcaattccatcccaaaaatctga---ttcttgttgctctttggacagGCTGGTCAGTTGCATCTTGTGAAACCATATATGGTTGCAGTTCAGAGTAACAATGTCTCTGCCATGAATGAAGCCTTGAATGAACTTTATGTCGAAGATG

upper sequence: LOC_Os11g01380.1 (Oryza sativa), 3'ss of exon 25
lower sequence: GRMZM2G091121_T01 (Zea mays), 3'ss of exon 5
gtttgtttcttatggcagggccttctattggtctatcagttttgctctgtttcaaaattttgaactgtttaattattatttgtacagGCTGGTCAGTTGCATCTTGTGAAACCATACATGGTTGCAGTTCAGAGCAACAATGTCTCTGCTGTGAATGAAGCTTTGAATGAGCTTTATGTTGAAGAGG
            | |  |  | ||  || |       | ||    ||  |  ||||| | |||    | |  ||  | |||| ||||||||||||||||||||||||||||||||| ||||||||||||||||| |||||||||||||| ||||||||||| |||||||| |||||||| ||||| |
-----------gtagt-gcactttgaatagaagccctatttcaattccatcccaaaaatctga---ttcttgttgctctttggacagGCTGGTCAGTTGCATCTTGTGAAACCATATATGGTTGCAGTTCAGAGTAACAATGTCTCTGCCGTGAATGAAGCCTTGAATGAACTTTATGTCGAAGATG

upper sequence: LOC_Os11g01380.1 (Oryza sativa), 3'ss of exon 25
lower sequence: GRMZM5G822591_T01 (Zea mays), 3'ss of exon 2
------------------gtttgtttcttatggcagggccttctattggtctatcagttttg---ctctgtttcaaaattttgaactgtttaattattatttgtacagGCTGGTCAGTTGCATCTTGTGAAACCATACATGGTTGCAGTTCAGAGCAACAATGTCTCTGCTGTGAATGAAGCTTTGAATGAGCTTTATGTTGAAGAGG
                   ||| |||| | | || |  | ||  || |         |||       ||    | ||| | |||  ||| |  ||  | |||| |||||||||||| |||||||||||||||||||| ||||||||||||||||| |||||||||||||||||||||||||| ||||| || ||||||||||||||||
gttagcatctgaatgaaaatttatttcct-tagc-gcactttggatagaagccctgttttcaaattccttcccccaaaatctgacttgtcttgttgctctttggacagGCTGGTCAATTGCATCTTGTGAAACCATATATGGTTGCAGTTCAGAGTAACAATGTCTCTGCTGTGAATGAAGCCTTGAACGAACTTTATGTTGAAGAGG

upper sequence: LOC_Os11g01380.1 (Oryza sativa), 3'ss of exon 25
lower sequence: GRMZM5G804382_T01 (Zea mays), 3'ss of exon 2
------------------gtttgtttcttatggcagggccttctattggtctatcagttttgctctgtttcaaaattttgaactgtttaattattatttgtacagGCTGGTCAGTTGCATCTTGTGAAACCATACATGGTTGCAGTTCAGAGCAACAATGTCTCTGCTGTGAATGAAGCTTTGAATGAGCTTTATGTTGAAGAGG
                   ||| |||| | | || |  | ||  || |         ||    |   || |||||| ||  ||||| |  ||  | |||| |||||||||||| |||||||||||||||||||| ||||||||||||||||| || ||||||||||||||||||||||| |||||||||||||||||||||||||
gttagcatctgaatggaaatttatttcct-tagc-gcactttgaatagaagccctgtttcaaattccttccaaaatctt--actgtcttgttgctctttggacagGCTGGTCAATTGCATCTTGTGAAACCATATATGGTTGCAGTTCAGAGTAATAATGTCTCTGCTGTGAATGAAGCCTTGAATGAGCTTTATGTTGAAGAGG

upper sequence: LOC_Os11g01380.1 (Oryza sativa), 3'ss of exon 25
lower sequence: GRMZM2G395549_T01 (Zea mays), 3'ss of exon 10
--------------gtttgtttcttatggcagggc-cttctattggtctatcagttttgctctgtttcaaaattttgaactgtttaattattatttgtacagGCTGGTCAGTTGCATCTTGTGAAACCATACATGGTTGCAGTTCAGAGCAACAATGTCTCTGCTGTGAATGAAGCTTTGAATGAGCTTTATGTTGAAGAGG-----------------------------------------------------------------------
              |    | | ||   |||| || |||  | | |     | ||||   |   |  ||||| | |||    | |  ||  | |||| ||||||||||||||||||||||||||||||||| ||||||||| ||||||| ||||||||||||||  |||||| ||| |||||||||||||||||   |||||                                                                       
gtaagcatctgattgaaaatctatttctgcagtgcactttgaatagaagccctgtttcaattcctcccaaaaatctga---ttcttgttgctctttggacaggctggtcagttgcatcttgtgaaaccatatatggttgcaattcagagtaacaatgtctctgccatgaatggagccttgaatgagctttatgtctgagagGAGGACTATGAGAGACTCCGTGAATCAGTTGACACGCATGACAACTTTGACCAGATTGGTCTTGCCCAGAAG

upper sequence: LOC_Os11g01380.1 (Oryza sativa), 3'ss of exon 25
lower sequence: GRMZM2G062042_T02 (Zea mays), 3'ss of exon 10
gtttgtttcttatggcagg----gccttctattggtctatcagtttt-gctctgtttcaaa---attttgaa---ctg--tttaattattatttgtacagGCTGGTCAGTTGCATCTTGTGAAACCATACATGGTTGCAGTTCAGAGCAACAATGTCTCTGCTGTGAATGAAGCTTTGAATGAGCTTTATGTTGAAGAGG
  |||   || |||  ||     ||| | | |||  || | | |    || |||||||||     |    ||   |||  | |  ||  | |||| ||||||||||||||||||||||||||||||||| ||||||||||||||||| |||||||||||||| ||||||||||| |||||||| |||||||| ||||| |
agttgaaactgatgaaagaaatagccctgttttgcactgtgaatagaagccctgtttcaattccgtcccaaaaatctgattcttgttgctctttggacagGCTGGTCAGTTGCATCTTGTGAAACCATATATGGTTGCAGTTCAGAGTAACAATGTCTCTGCCGTGAATGAAGCCTTGAATGAACTTTATGTCGAAGATG

upper sequence: LOC_Os11g01380.1 (Oryza sativa), 3'ss of exon 25
lower sequence: GLYMA11G06720.1 (Glycine max), 3'ss of exon 25
-------------------------------------gtttgtttcttat--ggcagggccttctattggtctatcagttttgctctgtttcaaaattttgaactgtttaattattatttgtacagGCTGGTCAGTTGCATCTTGTGAAACCATACATGGTTGCAGTTCAGAGCAACAATGTCTCTGCTGTGAATGAAGCTTTGAATGAGCTTTATGTTGAAGAGG
                                     ||||   ||||||  ||   |      |  |||  | | | |  |  || ||   || ||| |    || ||    ||| ||| | |||||||| ||  |     | || || || ||||||||||||||||| ||||||||||| |||||||| ||||| |||||||||||  |||||| ||| || |
gtctgcaattttcataccctattgtcaaatgcctacggtttcaatcttatttggtgagataacttgctggctt-taaatgctattcagtaataatattgtttgttgcttgg--attttttattcagGCTGGCCACCTCAGATTAGTTAAGCCGTACATGGTTGCAGTTCAAAGCAACAATGTGTCTGCTGTCAATGAGGCTTTGAATGAAATTTATGCTGAGGAAG

upper sequence: LOC_Os11g01380.1 (Oryza sativa), 3'ss of exon 25
lower sequence: GLYMA02G42560.1 (Glycine max), 3'ss of exon 25
gtttgtttcttatggcagggccttctattggtctatcagttttgctctgtttcaaaattt-tgaactgtttaattattatttg-tacagGCTGGTCAGTTGCATCTTGTGAAACCATACATGGTTGCAGTTCAGAGCAACAATGTCTCTGCTGTGAATGAAGCTTTGAATGAGCTTTATGTTGAAGAGG
||  | |  |||  |       ||  ||| |  ||| |||| |    ||    ||   |  ||      || | | | || || || ||||||||||  | | ||||||||||||||| |||||||||||||| |||||||| || |||||||| |||||||| ||||||||| | |||||||| ||||
gtaggatcattagtggtaaaaatttaattaga-tattagttgttgcatgccataactctaatgggaaacttcactttaatatgctatagGCTGGTCACCTCCGTCTTGTGAAACCATATATGGTTGCAGTTCAAAGCAACAACGTATCTGCTGTTAATGAAGCGTTGAATGAGATATATGTTGAGGAGG

upper sequence: LOC_Os11g01380.1 (Oryza sativa), 3'ss of exon 25
lower sequence: GLYMA18G02960.1 (Glycine max), 3'ss of exon 24
----gtttgtttcttatggcagggccttcta-----ttggtctatcagttttgctctgtttcaaaattttgaactgtttaattattatttgt-acagGCTGGTCAGTTGCATCTTGTGAAACCATACATGGTTGCAGTTCAGAGCAACAATGTCTCTGCTGTGAATGAAGCTTTGAATGAGCTTTATGTTGAAGAGG
      ||  | ||     ||    | |||      ||  | ||| |  | |  ||  |||||    | ||||   |||   | | || | | | ||||||||||  | | |||||| || ||||||||||||||||||||||| |||||||| |||||||| ||||||||  | |||||  | |||||||| ||||
gtagcattaatactgtcaacaatttcatcttaatttttactttataacctgttttccatttcact-ctatgaatattttccctgtgatgtattatagGCTGGTCATCTCCGTCTTGTCAAGCCATACATGGTTGCAGTTCAGAGTAACAATGTGTCTGCTGTTAATGAAGCCCTTAATGAAATATATGTTGAGGAGG

upper sequence: LOC_Os11g01380.1 (Oryza sativa), 3'ss of exon 25
lower sequence: GLYMA14G06340.1 (Glycine max), 3'ss of exon 25
gtttgtttcttatggcagggccttctattggtctatcagttttgctctgtttcaaaattt-tgaactgtttaattattatttgtacagGCTGGTCAGTTGCATCTTGTGAAACCATACATGGTTGCAGTTCAGAGCAACAATGTCTCTGCTGTGAATGAAGCTTTGAATGAGCTTTATGTTGAAGAGG
||  | |   ||| |       ||  ||| |  |||||||| |    ||    || | |  ||     ||| |||  |||   || ||||||||||  | | |||||||||||| || ||| |||||||||| ||||||||||| |||||||| |||||||| ||||||||| | ||||| || ||||
gtaggatgaatattggcaaaaatttcattaga-tatcagttgttgcatgccataacactaatgggaaatttcattgatatgc-tatagGCTGGTCACCTCCGTCTTGTGAAACCGTATATGATTGCAGTTCAAAGCAACAATGTATCTGCTGTTAATGAAGCGTTGAATGAGATATATGTCGAGGAGG

upper sequence: LOC_Os11g01380.1 (Oryza sativa), 3'ss of exon 25
lower sequence: GLYMA02G39360.1 (Glycine max), 3'ss of exon 25
-----------------------------------gtttgtttcttatggcagggccttctattggtctatcagttttgctctgtttcaaaattttgaactgtttaattattatttgta-----cagGCTGGTCAGTTGCATCTTGTGAAACCATACATGGTTGCAGTTCAGAGCAACAATGTCTCTGCTGTGAATGAAGCTTTGAATGAGCTTTATGTTGAAGAGG
                                   || |   ||||||    | |   | || |   |  ||     |  | | |  ||| ||| | |  ||||   | ||| ||| |       ||||||| ||  | |   | || || || ||| || |||||||||| ||||| ||||| |||||||| |||||||||||||||||  |||||||||| ||||
gtctgtatgtctcagtctgttttctaatgtgttaagtcttaatcttattttggtgaggt-taataaccgttcgaaaatattttatg-caatattcttatttgttgcttgattttttatggtttttagGCTGGCCACATTCGATTGGTTAAGCCGTACTTGATTGCAGTTCAAAGCAATAATGTGTCTGCTGTTAATGAAGCTTTGAATGAAATTTATGTTGAGGAGG

upper sequence: LOC_Os11g01380.1 (Oryza sativa), 3'ss of exon 25
lower sequence: GLYMA14G37510.1 (Glycine max), 3'ss of exon 23
----------------------gtttgtttcttatggcagggccttctattggtc-------tatcagttttgctctgttt----caaaattttgaactgtttaattattatttgta-----cagGCTGGTCAGTTGCATCTTGTGAAACCATACATGGTTGCAGTTCAGAGCAACAATGTCTCTGCTGTGAATGAAGCTTTGAATGAGCTTTATGTTGAAGAGG
                        |  | | ||| |       ||||| |||||        || | ||||     | |||    ||| ||| | |  ||||   | ||| ||| |       ||||||| ||  | |   | || || || ||| ||||||||||||| ||||| ||||| |||||||| |||||||||||||||||  |||||||||| ||||
gtctgtaggtctcattctattttctaatgtgttaagttttaatcttcttttggtgaagttaataactgtttgaaaatattttatgcaatattcttatttgttgcttgattttttctggtttttagGCTGGCCACATCCGATTGGTTAAGCCGTACTTGGTTGCAGTTCAAAGCAATAATGTGTCTGCTGTTAATGAAGCTTTGAATGAAATTTATGTTGAGGAGG

upper sequence: LOC_Os11g01380.1 (Oryza sativa), 3'ss of exon 25
lower sequence: GLYMA11G35460.1 (Glycine max), 3'ss of exon 24
gtttgtttctta-tggcagggccttc-tattggtctatcagttttgctctgtttcaaaattt-----tgaactgtttaattattatttgt-acagGCTGGTCAGTTGCATCTTGTGAAACCATACATGGTTGCAGTTCAGAGCAACAATGTCTCTGCTGTGAATGAAGCTTTGAATGAGCTTTATGTTGAAGAGG
||    ||  || || ||     ||| | || || | |   || |   ||||||   | ||      ||||   |||   | | || | | | ||||||||||  | | |||||| || || |||||||||||||||||||| ||||| || |||||||| ||||||||  |||||||  | |||||||| ||||
gtagcattaatactgtcaacaatttcattttagtttttactttataacctgttttccatttcactgatgaatattttccctgtgatgtattatagGCTGGTCATCTCCGTCTTGTCAAGCCTTACATGGTTGCAGTTCAGAGTAACAACGTGTCTGCTGTTAATGAAGCCCTGAATGAAATATATGTTGAGGAGG

upper sequence: LOC_Os11g01380.1 (Oryza sativa), 3'ss of exon 25
lower sequence: GLYMA01G38580.1 (Glycine max), 3'ss of exon 25
------------------------------------gtttgtttcttat--ggcagggccttctattggtctatcagttttgctctgtttcaaaattttgaactgtttaattattatttgtacagGCTGGTCAGTTGCATCTTGTGAAACCATACATGGTTGCAGTTCAGAGCAACAATGTCTCTGCTGTGAATGAAGCTTTGAATGAGCTTTATGTTGAAGAGG
                                    ||||   ||||||  ||   |    | |  |||| |   | |  |  |||||   |  ||| |    || ||   | || | | | |||||||| ||  |     | || || || ||||||||||||||||| ||||||||||| || ||||| |||||||||||||||||  |||||||||| || |
gtctgcaatttcataccctattgccaaatggctacagtttcaatcttatttggagagataatttgctggttt-caaatgctattctgtaatagtattgtttgttgcttggattttttattttcagGCTGGCCACCTTAGATTAGTTAAGCCGTACATGGTTGCAGTTCAAAGCAACAATGTGTCCGCTGTCAATGAAGCTTTGAATGAAATTTATGTTGAGGAAG

upper sequence: LOC_Os11g01380.1 (Oryza sativa), 3'ss of exon 25
lower sequence: AT3G08530.1 (Arabidopsis thaliana), 3'ss of exon 25
gtttgtttcttatggcagggccttctattggtctatcagttttgctctgtttcaaaattttgaactgtttaattattatttgtacagGCTGGTCAGTTGCATCTTGTGAAACCATACATGGTTGCAGTTCAGAGCAACAATGTCTCTGCTGTGAATGAAGCTTTGAATGAGCTTTATGTTGAAGAGG
||| |   || |  | | | | || | ||  ||||| |      ||  | | ||  | ||  |||  ||   || || |     ||||||||||| |||| |||| | || ||||||||| ||||||||||||||||||||||||||||||| ||||| ||| |||||||| | || || ||||| |
gttagaagctgactg-atgactttgtttttttctataaaaacaactgagctacattactt--aacaattggtttcttctgatctcagGCTGGTCACTTGCGTCTTATCAAGCCATACATGATTGCAGTTCAGAGCAACAATGTCTCTGCTGTTAATGAGGCTCTGAATGAGATATACGTGGAAGAAG

upper sequence: LOC_Os11g01380.1 (Oryza sativa), 3'ss of exon 25
lower sequence: AT3G11130.1 (Arabidopsis thaliana), 3'ss of exon 25
------gtttgtttcttatggcagggccttctattggtctatcagttttgctctgtttcaaaattttgaactgtt---taattattatttgta----cagGCTGGTCAGTTGCATCTTGTGAAACCATACATGGTTGCAGTTCAGAGCAACAATGTCTCTGCTGTGAATGAAGCTTTGAATGAGCTTTATGTTGAAGAGG
      |  ||    ||     |     |||| ||      | |       |  | || | ||| |  | ||| |   || || || ||| |     ||||||||||| ||||  ||| | || ||||| |||||||||||||||||||| ||||| |||||||| ||||||||| |||||||| | ||||  ||||| |
gttagaggctgaccattgatttaatattttctgttaaaaacttatcaccagtg-gcttaacaatctatatctgatgattatttcttgtttctgatctcagGCTGGTCACTTGCGCCTTATTAAGCCATATATGGTTGCAGTTCAGAGCAATAATGTATCTGCTGTAAATGAAGCTCTGAATGAGATATATGCAGAAGAAG

upper sequence: LOC_Os11g01380.1 (Oryza sativa), 3'ss of exon 25
lower sequence: Vv13s0067g01290.t01 (Vitis vinifera), 3'ss of exon 25
----------------------------gtttgtttcttatggcagggccttctattggtcta-tcagttttgctctgtttcaaaattttgaactgtttaattattatttgta------cagGCTGGTCAGTTGCATCTTGTGAAACCATACATGGTTGCAGTTCAGAGCAACAATGTCTCTGCTGTGAATGAAGCTTTGAATGAGCTTTATGTTGAAGAGG
                              ||  ||||| |      |  |  || | || |  |    | | ||     |  |  |  |    || |||    || |||||       ||||| |||||  | ||||||||||| ||||| ||||||||||||||||| |||||||| |||||||||||||| |||||||||| | |||||||||| ||||
gtttttgtttgtgctggcttttttgtttcctttcttcttcttctgaagtatgttacttgtttccttgactcttctagacgtttatgtactcttttggttatgcgttttttgttggattccagGCAGGTCACCTTCATCTTGTGAAGCCATATATGGTTGCAGTTCAGAGTAACAATGTTTCTGCTGTGAATGAGGCTTTGAATGGGATTTATGTTGAGGAGG

Mapped EST sequences

Showing partial alignments of ESTs and genomic sequences. See full alignments


 ATGC     EST sequence
 ATGC     genomic sequence (exon)
 ATGC     genomic sequence (truncated intron)


EST: gi|29624172|gb|CB629183.1|CB629183
EST:     TACTTGCGCTTCGTTTGGATCATACAAGAGTCGTGGACATAATGCGCAAG                         GCTGGTCAGTTGCATCTTGTGAAACCATACATGGTTGCAGTTCAGAGCAAC
genomic: TACTTGCGCTTCGTTTGGATCATACAAGAGTCGTGGACATAATGCGCAAGgtttgtttct ... atttgtacagGCTGGTCAGTTGCATCTTGTGAAACCATACATGGTTGCAGTTCAGAGCAAC
EST: gi|12622957|gb|AU173170.1|AU173170
EST:     GGATCATACAAGAGTCGTGGACATAATGCGCAAG                         GCTGGTCAGTTGCATCTTGTGAAACCATACATGGTTGCAGTTCAGAGCAAC
genomic: GGATCATACAAGAGTCGTGGACATAATGCGCAAGgtttgtttct ... atttgtacagGCTGGTCAGTTGCATCTTGTGAAACCATACATGGTTGCAGTTCAGAGCAAC
EST: gi|5005228|gb|AU070390.1|AU070390
EST:     CAAGAGTCGTGGACATAATGCGCAAG                         GCTGGTCAGTTGCATCTTGTGAAACCATACATGGTTGCAGTTCAGAGCAAC
genomic: CAAGAGTCGTGGACATAATGCGCAAGgtttgtttct ... atttgtacagGCTGGTCAGTTGCATCTTGTGAAACCATACATGGTTGCAGTTCAGAGCAAC
EST: gi|29685119|gb|CB681394.1|CB681394
EST:     GGATCATACAAGAGCCCTGGACATAATGCGCAAG                         GCTGGTCAGTTGCATCTTGTGAAACCATACATGGTTGCAGTTCAGAGCAAC
genomic: GGATCATACAAGAGTCGTGGACATAATGCGCAAGgtttgtttct ... atttgtacagGCTGGTCAGTTGCATCTTGTGAAACCATACATGGTTGCAGTTCAGAGCAAC
EST: gi|29664581|gb|CB660856.1|CB660856
EST:     TACTTGCGCTTCGTTTGGATCATACAAGAGTCGTGGACATAATGCGCAAG                         GCTGGTCAGTTGCATCTTGTGAAACCATACATGGTTGCAGTTCAGAGCAAC
genomic: TACTTGCGCTTCGTTTGGATCATACAAGAGTCGTGGACATAATGCGCAAGgtttgtttct ... atttgtacagGCTGGTCAGTTGCATCTTGTGAAACCATACATGGTTGCAGTTCAGAGCAAC
EST: gi|87017011|gb|CI286147.1|CI286147
EST:     TACTTGCGCTTCGTTTGGATCATACAAGAGTCGTGGACATAATGCGCAAG                         GCTGGTCAGTTGCATCTTGTGAAACCATACATGGTTGCAGTTCAGAGCAAC
genomic: TACTTGCGCTTCGTTTGGATCATACAAGAGTCGTGGACATAATGCGCAAGgtttgtttct ... atttgtacagGCTGGTCAGTTGCATCTTGTGAAACCATACATGGTTGCAGTTCAGAGCAAC

RNA-Seq data


 ATGC   Supported by RNA-Seq exonic block that spans over the splice site

 atgs   Truncated intron sequence

Each block is as long as the maximal overhang of any read spanning the junction.
The score is the number of alignments spanning the junction.


Found data for 1 RNA-Seqlibrary.


Block sizes: 72 (upstream exon), 75 (downstream exon)
Score: 84

GCACTTCTATCTGCAAGAGCATCCTGATCTCATCAATGACCTTCTCAATGTACTTGCGCTTCGTTTGGATCATACAAGAGTCGTGGACATAATGCGCAAGgtttgtttct ... atttgtacagGCTGGTCAGTTGCATCTTGTGAAACCATACATGGTTGCAGTTCAGAGCAACAATGTCTCTGCTGTGAATGAAGCTTTGAATGAGCTTTATGTTGAAGAGG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ctatcagttttgctctgtttcaaaattttgaactgtttaattattatttgtacagGCTGGTCAGTTGCATCTTGTGAAACCATACATGGTTGCAGTTCAGAGCAACAATGTCTCTGCTGTGAATGAAGCTTTGAATGAGCTTTATGTTGAAGAGG
                                  gtttaat  putative branch site (score: 84)
                 tttcaaaattttgaac  TA-rich tract
















Putative cis-regulatory sequences

 atgc intron ATGC exonic elements by Pertea et al.
 ATGC exon atgc putative intronic elements
 ATGC putative exonic elements identified for retained introns
        10        20        30        40        50        60        70        80        90        100       110       120       130       140       150       160       170       180       190       200       210       220 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtttgtttcttatggcagggccttctattggtctatcagttttgctctgtttcaaaattttgaactgtttaattattatttgtacagGCTGGTCAGTTGCATCTTGTGAAACCATACATGGTTGCAGTTCAGAGCAACAATGTCTCTGCTGTGAATGAAGCTTTGAATGAGCTTTATGTTGAAGAGG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGCTT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAGG