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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gttagcatctgaatggaaatttatttccttagcgcactttgaatagaagccctgtttcaaattccttccaaaatcttactgtcttgttgctctttggacagGCTGGTCAATTGCATCTTGTGAAACCATATATGGTTGCAGTTCAGAGTAATAATGTCTCTGCTGTGAATGAAGCCTTGAATGAGCTTTATGTTGAAGAGG

Basic information

species Zea mays
transcript GRMZM5G804382_T01
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


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

upper sequence: GRMZM5G804382_T01 (Zea mays), 3'ss of exon 2
lower sequence: LOC_Os12g01390.1 (Oryza sativa), 3'ss of exon 25
gttagcatctgaatggaaatttatttcct-tagc-gcactttgaatagaagccctgtttcaaattccttccaaaatctt--actgtcttgttgctctttggacagGCTGGTCAATTGCATCTTGTGAAACCATATATGGTTGCAGTTCAGAGTAATAATGTCTCTGCTGTGAATGAAGCCTTGAATGAGCTTTATGTTGAAGAGG
                   ||| |||| | | || |  | ||  || |         ||    | | || |||||| ||  ||| | |  ||  |||||| |||||||||||| |||||||||||||||||||| ||||||||||||||||| || ||||||||||||||||||||| | |||||||||||||||||||||||||
------------------gtttgtttcttatggcagggccttctattggtctatcagttttgctccgtttcaaaattttgaactatttcattattctttgtacagGCTGGTCAGTTGCATCTTGTGAAACCATACATGGTTGCAGTTCAGAGCAACAATGTCTCTGCTGTGAATGAATCTTTGAATGAGCTTTATGTTGAAGAGG

upper sequence: GRMZM5G804382_T01 (Zea mays), 3'ss of exon 2
lower sequence: GLYMA11G06720.1 (Glycine max), 3'ss of exon 25
------------gttagcatctgaatggaaatttatttccttagcgcactttgaatagaagccctgtt----tcaaattccttccaa-aatcttactgtcttgttgctc------tttggacagGCTGGTCAATTGCATCTTGTGAAACCATATATGGTTGCAGTTCAGAGTAATAATGTCTCTGCTGTGAATGAAGCCTTGAATGAGCTTTATGTTGAAGAGG
              || | | |      |    ||     | |      ||||   |||   | || |    | |||| |  | ||  |||  || ||| ||||||||       |||   |||||||| ||  |     | || || || || |||||||||||||| || || ||||| |||||||| ||||| || ||||||||  |||||| ||| || |
gtctgcaattttcataccctattgtcaaatgcctacggtttcaatcttatttggtgagataacttgctggctttaaatgctattcagtaataatattgt-ttgttgcttggattttttattcagGCTGGCCACCTCAGATTAGTTAAGCCGTACATGGTTGCAGTTCAAAGCAACAATGTGTCTGCTGTCAATGAGGCTTTGAATGAAATTTATGCTGAGGAAG

upper sequence: GRMZM5G804382_T01 (Zea mays), 3'ss of exon 2
lower sequence: GLYMA02G42560.1 (Glycine max), 3'ss of exon 25
gttagcatc-tgaatggaaatttatttccttagcgcactttgaatagaagccctgtttcaaattccttccaaaatcttactgtcttgttgctctttggacagGCTGGTCAATTGCATCTTGTGAAACCATATATGGTTGCAGTTCAGAGTAATAATGTCTCTGCTGTGAATGAAGCCTTGAATGAGCTTTATGTTGAAGAGG
  ||| ||| | | ||| ||   ||||  ||||       |   |  | ||| |   || |||        |||  | ||| |  | | |||      | ||||||||||  | | |||||||||||||||||||||||||||||| || || || || |||||||| |||||||| ||||||||| | |||||||| ||||
-gtaggatcattagtggtaaaa-atttaattagatattagttgttgcatgccataactctaatg-----ggaaacttcactttaatat-gct------atagGCTGGTCACCTCCGTCTTGTGAAACCATATATGGTTGCAGTTCAAAGCAACAACGTATCTGCTGTTAATGAAGCGTTGAATGAGATATATGTTGAGGAGG

upper sequence: GRMZM5G804382_T01 (Zea mays), 3'ss of exon 2
lower sequence: GLYMA18G02960.1 (Glycine max), 3'ss of exon 24
gttagcatctgaatggaaatttatttccttagcgcactttgaatagaagccctgtttcaaattccttccaaaatcttactgtcttgttgctctttggacagGCTGGTCAATTGCATCTTGTGAAACCATATATGGTTGCAGTTCAGAGTAATAATGTCTCTGCTGTGAATGAAGCCTTGAATGAGCTTTATGTTGAAGAGG
  ||||||    |  |  |   ||||| |      | ||| | |  |   |||||||   ||| |   | |    |   |  | |||      ||  | ||||||||||  | | |||||| || ||||| |||||||||||||||||||| ||||| |||||||| ||||||||| | |||||  | |||||||| ||||
-gtagcattaatactgtcaacaatttcatc--ttaatttttactttataacctgttttccatttcactctatgaatattttccctgtgatgtatt--atagGCTGGTCATCTCCGTCTTGTCAAGCCATACATGGTTGCAGTTCAGAGTAACAATGTGTCTGCTGTTAATGAAGCCCTTAATGAAATATATGTTGAGGAGG

upper sequence: GRMZM5G804382_T01 (Zea mays), 3'ss of exon 2
lower sequence: GLYMA14G06340.1 (Glycine max), 3'ss of exon 25
gttagcatctgaatggaaatttatttccttagcgcactttgaatagaagccctgtttcaaattccttccaaaatcttactgtcttgttgctctttggacagGCTGGTCAATTGCATCTTGTGAAACCATATATGGTTGCAGTTCAGAGTAATAATGTCTCTGCTGTGAATGAAGCCTTGAATGAGCTTTATGTTGAAGAGG
  ||| ||    || |  |   ||||| ||||    |  |   |  | ||| |    | |||        |||| | | ||   || |         | ||||||||||  | | |||||||||||| |||||| |||||||||| || || ||||| |||||||| |||||||| ||||||||| | ||||| || ||||
-gtaggatgaatattggcaaaaatttcattagatatcagttgttgcatgccataacactaatg-----ggaaatttcattgatatgct---------atagGCTGGTCACCTCCGTCTTGTGAAACCGTATATGATTGCAGTTCAAAGCAACAATGTATCTGCTGTTAATGAAGCGTTGAATGAGATATATGTCGAGGAGG

upper sequence: GRMZM5G804382_T01 (Zea mays), 3'ss of exon 2
lower sequence: GLYMA14G37510.1 (Glycine max), 3'ss of exon 23
--------gttagcatctgaatggaaatttattt--ccttagcgcactttgaatagaagcc----ctgtttcaaattcctt----ccaaaatcttact-gt--cttgttgctctttggac---agGCTGGTCAATTGCATCTTGTGAAACCATATATGGTTGCAGTTCAGAGTAATAATGTCTCTGCTGTGAATGAAGCCTTGAATGAGCTTTATGTTGAAGAGG
        ||     |||   |   ||| | ||     |||     ||||   |  |        |||||| ||| |  ||    | | | ||||| | ||  |||| |  | | |||     ||||||| ||  | |   | || || || ||  ||||||||||||| || |||||||| |||||||| |||||||| ||||||||  |||||||||| ||||
gtctgtaggtctcattctattttctaatgtgttaagttttaatcttcttttggtgaagttaataactgtttgaaaatattttatgcaatattcttatttgttgcttgattttttctggtttttagGCTGGCCACATCCGATTGGTTAAGCCGTACTTGGTTGCAGTTCAAAGCAATAATGTGTCTGCTGTTAATGAAGCTTTGAATGAAATTTATGTTGAGGAGG

upper sequence: GRMZM5G804382_T01 (Zea mays), 3'ss of exon 2
lower sequence: GLYMA11G35460.1 (Glycine max), 3'ss of exon 24
gttagcatctgaatggaaatttatttccttagcgcactttgaatagaagccctgtttcaaattccttccaaaatcttactgtcttgttgctctttggacagGCTGGTCAATTGCATCTTGTGAAACCATATATGGTTGCAGTTCAGAGTAATAATGTCTCTGCTGTGAATGAAGCCTTGAATGAGCTTTATGTTGAAGAGG
  ||||||    |  |  |   ||||| ||   |   |||   |   | ||   |||| | |||  |    ||| ||       || ||   |    | ||||||||||  | | |||||| || || || |||||||||||||||||||| || || |||||||| ||||||||| |||||||  | |||||||| ||||
-gtagcattaatactgtcaacaatttcattttagt-ttttactttataacctgttttccatttcactgatgaatattttccctgtgatgtatt----atagGCTGGTCATCTCCGTCTTGTCAAGCCTTACATGGTTGCAGTTCAGAGTAACAACGTGTCTGCTGTTAATGAAGCCCTGAATGAAATATATGTTGAGGAGG

upper sequence: GRMZM5G804382_T01 (Zea mays), 3'ss of exon 2
lower sequence: GLYMA01G38580.1 (Glycine max), 3'ss of exon 25
--------gttagcatctgaatggaaatttatttc---cttagcgcactttgaatagaagccctg----tttcaaattcc-ttccaaaatcttactgtcttgttgctc----tttgga----cagGCTGGTCAATTGCATCTTGTGAAACCATATATGGTTGCAGTTCAGAGTAATAATGTCTCTGCTGTGAATGAAGCCTTGAATGAGCTTTATGTTGAAGAGG
         ||   | |  | ||  || |   | |    | |      |||| | |||     ||    |||||||| |  |||   |||  || ||| ||||||||     |||  |    |||||||| ||  |     | || || || || |||||||||||||| || || ||||| || ||||| |||||||| ||||||||  |||||||||| || |
gtctgcaatttcataccctattgccaaatggctacagtttcaatcttatttggagagataatttgctggtttcaaatgctattctgtaatagtattgt-ttgttgcttggattttttattttcagGCTGGCCACCTTAGATTAGTTAAGCCGTACATGGTTGCAGTTCAAAGCAACAATGTGTCCGCTGTCAATGAAGCTTTGAATGAAATTTATGTTGAGGAAG

upper sequence: GRMZM5G804382_T01 (Zea mays), 3'ss of exon 2
lower sequence: AT3G08530.1 (Arabidopsis thaliana), 3'ss of exon 25
gttagcatctgaatggaaatttatttccttagcgcactttgaatagaagccctgtttcaaattccttccaaaatcttactgtcttgttgctctttggacagGCTGGTCAATTGCATCTTGTGAAACCATATATGGTTGCAGTTCAGAGTAATAATGTCTCTGCTGTGAATGAAGCCTTGAATGAGCTTTATGTTGAAGAGG
||||| | |||| ||   | ||  ||  ||      || | || | ||   |||    | ||| |||   ||   ||  | ||||  || |||     ||||||||||| |||| |||| | || ||||| ||| ||||||||||||| || |||||||||||||| ||||| ||  |||||||| | || || ||||| |
gttagaagctgactgatgactttgttttttt-----ctataaaaacaa---ctgagctacattacttaacaa---ttggtttctt-ctgatct-----cagGCTGGTCACTTGCGTCTTATCAAGCCATACATGATTGCAGTTCAGAGCAACAATGTCTCTGCTGTTAATGAGGCTCTGAATGAGATATACGTGGAAGAAG

upper sequence: GRMZM5G804382_T01 (Zea mays), 3'ss of exon 2
lower sequence: AT3G11130.1 (Arabidopsis thaliana), 3'ss of exon 25
gttagcatctgaatggaaatttatt--tccttagcgcactttgaatagaagccctgtttcaaattccttccaaaatcttactgtcttgttgctctttggacagGCTGGTCAATTGCATCTTGTGAAACCATATATGGTTGCAGTTCAGAGTAATAATGTCTCTGCTGTGAATGAAGCCTTGAATGAGCTTTATGTTGAAGAGG
|||||   ||||      ||||| |  |   |     |   | |  |  ||    | || | | ||  |     ||  |  | ||||||| ||  |    ||||||||||| ||||  ||| | || ||||||||||||||||||||||| |||||||| |||||||| ||||||||  |||||||| | ||||  ||||| |
gttagaggctgaccattgatttaatattttctgttaaaaacttatcaccagtg--gcttaacaatctatatctgatgattatttcttgtttctgatct--cagGCTGGTCACTTGCGCCTTATTAAGCCATATATGGTTGCAGTTCAGAGCAATAATGTATCTGCTGTAAATGAAGCTCTGAATGAGATATATGCAGAAGAAG

upper sequence: GRMZM5G804382_T01 (Zea mays), 3'ss of exon 2
lower sequence: Vv06s0004g06860.t01 (Vitis vinifera), 3'ss of exon 25
-------------gttagcatctg---aatggaaatt--tatttccttagcgcactttgaatagaagccct---gtttcaaattccttcca------aaatcttactgtcttgttgctctttgga---cagGCTGGTCAATTGCATCTTGTGAAACCATATATGGTTGCAGTTCAGAGTAATAATGTCTCTGCTGTGAATGAAGCCTTGAATGAGCTTTATGTTGAAGAGG
              |||   | |     ||||| |||  | | | |||     | |  ||| | | |       |||| ||| |  ||           ||||||   |  || | ||||||||    |||||||||||  | ||||||||||| || ||||||||||| |||||||||| ||||||  |||| || |||||||| || ||||   || |||| || ||||
gtctgcatgtttgcttactctttatgtgatggatattgctgtgtgcttcttttagtgggaacaaatgattaaaagtttaaaaatggttttgtcaatggtatcttatgcttatgat-ctctttgggtttcagGCTGGTCACCTTCATCTTGTGAAGCCCTATATGGTTGCTGTTCAGAGTACTAATGTGGCTGCGGTAAATGAAGCATTAAATGGTATTCATGTAGAGGAGG

upper sequence: GRMZM5G804382_T01 (Zea mays), 3'ss of exon 2
lower sequence: Vv13s0067g01290.t01 (Vitis vinifera), 3'ss of exon 25
gttagcatctgaatggaaattt--atttccttagcgcacttt---gaatagaagccctgtttca--aattccttccaaaatct---tactgtcttg--------ttgctctttgga---cagGCTGGTCAATTGCATCTTGTGAAACCATATATGGTTGCAGTTCAGAGTAATAATGTCTCTGCTGTGAATGAAGCCTTGAATGAGCTTTATGTTGAAGAGG
|||    | ||    |   |||   |||||||    |   ||    | ||     | ||||||    | || |    |  | |   |||| | |||        ||  |  |||||   ||||| |||||  | ||||||||||| |||||||||||||||||||||||||| ||||| |||||||||||||| || ||||||| | |||||||||| ||||
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|32846997|gb|CD986678.1|CD986678
EST:     TGCTTGCACTTCGTTTAGATCATACCAGAGTTGTAGACATAATGCGCAAG                         GCTGGTCAATTGCATCTTGTGAAACCATATATGGTTGCAGTTCAGAGTAAT
genomic: TGCTTGCACTTCGTTTAGATCATACCAGAGTTGTAGACATAATGCGCAAGgttagcatct ... ctttggacagGCTGGTCAATTGCATCTTGTGAAACCATATATGGTTGCAGTTCAGAGTAAT
EST: gi|32929767|gb|CF034579.1|CF034579
EST:     TGCTTGCACTTCGTTTAGATCATACCAGAGTTGTAGACATAATGCGCAAG                         GCTGGTCAATTGCATCTTGTGAAACCATATATGGTTGCAGTTCAGAGTAAT
genomic: TGCTTGCACTTCGTTTAGATCATACCAGAGTTGTAGACATAATGCGCAAGgttagcatct ... ctttggacagGCTGGTCAATTGCATCTTGTGAAACCATATATGGTTGCAGTTCAGAGTAAT
EST: gi|32848265|gb|CD987946.1|CD987946
EST:     TGCTTGCACTTCGTTTAGATCATACCAGAGTTGTAGACATAATGCGCAAG                         GCTGGTCAATTGCATCTTGTGAAACCATATATGGTTGCAGTTCAGAGTAAT
genomic: TGCTTGCACTTCGTTTAGATCATACCAGAGTTGTAGACATAATGCGCAAGgttagcatct ... ctttggacagGCTGGTCAATTGCATCTTGTGAAACCATATATGGTTGCAGTTCAGAGTAAT
EST: gi|89761296|gb|DY689368.1|DY689368
EST:     TGCTTGCACTTCGTTTAGATCATACCAGAGTTGTAGACATAATGCGCAAG                         GCTGGTCAATTGCATCTTGTGAAACCATATATGGTTGCAGTTCAGAGTAAT
genomic: TGCTTGCACTTCGTTTAGATCATACCAGAGTTGTAGACATAATGCGCAAGgttagcatct ... ctttggacagGCTGGTCAATTGCATCTTGTGAAACCATATATGGTTGCAGTTCAGAGTAAT
EST: gi|71765800|gb|DR963737.1|DR963737
EST:     TGCTTGCACTTCGTTTAGATCATACCAGAGTTGTAGACATAATGCGCAAG                         GCTGGTCAATTGCATCTTGTGAAACCATATATGGTTGCAGTTCAGAGTAAT
genomic: TGCTTGCACTTCGTTTAGATCATACCAGAGTTGTAGACATAATGCGCAAGgttagcatct ... ctttggacagGCTGGTCAATTGCATCTTGTGAAACCATATATGGTTGCAGTTCAGAGTAAT

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 4 RNA-Seq libraries.


Block sizes: 49 (upstream exon), 47 (downstream exon)
Score: 233

TCACTTCTATTTGCAAGAGCATCCTGATCTCATCAATGATATGCTGAATGTGCTTGCACTTCGTTTAGATCATACCAGAGTTGTAGACATAATGCGCAAGgttagcatct ... ctttggacagGCTGGTCAATTGCATCTTGTGAAACCATATATGGTTGCAGTTCAGAGTAATAATGTCTCTGCTGTGAATGAAGCCTTGAATGAGCTTTATGTTGAAGAGG


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 203

TCACTTCTATTTGCAAGAGCATCCTGATCTCATCAATGATATGCTGAATGTGCTTGCACTTCGTTTAGATCATACCAGAGTTGTAGACATAATGCGCAAGgttagcatct ... ctttggacagGCTGGTCAATTGCATCTTGTGAAACCATATATGGTTGCAGTTCAGAGTAATAATGTCTCTGCTGTGAATGAAGCCTTGAATGAGCTTTATGTTGAAGAGG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 318

TCACTTCTATTTGCAAGAGCATCCTGATCTCATCAATGATATGCTGAATGTGCTTGCACTTCGTTTAGATCATACCAGAGTTGTAGACATAATGCGCAAGgttagcatct ... ctttggacagGCTGGTCAATTGCATCTTGTGAAACCATATATGGTTGCAGTTCAGAGTAATAATGTCTCTGCTGTGAATGAAGCCTTGAATGAGCTTTATGTTGAAGAGG


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 262

TCACTTCTATTTGCAAGAGCATCCTGATCTCATCAATGATATGCTGAATGTGCTTGCACTTCGTTTAGATCATACCAGAGTTGTAGACATAATGCGCAAGgttagcatct ... ctttggacagGCTGGTCAATTGCATCTTGTGAAACCATATATGGTTGCAGTTCAGAGTAATAATGTCTCTGCTGTGAATGAAGCCTTGAATGAGCTTTATGTTGAAGAGG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aagccctgtttcaaattccttccaaaatcttactgtcttgttgctctttggacagGCTGGTCAATTGCATCTTGTGAAACCATATATGGTTGCAGTTCAGAGTAATAATGTCTCTGCTGTGAATGAAGCCTTGAATGAGCTTTATGTTGAAGAGG
                          atcttac  putative branch site (score: 262)
                                   tcttgttgctcttt  putative PPT
        tttcaaatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gttagcatctgaatggaaatttatttccttagcgcactttgaatagaagccctgtttcaaattccttccaaaatcttactgtcttgttgctctttggacagGCTGGTCAATTGCATCTTGTGAAACCATATATGGTTGCAGTTCAGAGTAATAATGTCTCTGCTGTGAATGAAGCCTTGAATGAGCTTTATGTTGAAGAGG

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