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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtagctattttcatactcgtgtacagatctgagctttgaacaatttgtacatcagtcactaagttgctgttctatgccagGACTTTAAGATTCAGAATATTGTTGGCTCTTGTGATGTAAAGTTTCCAATTAGGCTTGAGGGCCTTGCCTATTCTCATGGTGCCTTCTCAAGT

Basic information

species Zea mays
transcript GRMZM2G149238_T04
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G149238_T04 (Zea mays), 3'ss of exon 5
lower sequence: LOC_Os12g39070.1 (Oryza sativa), 3'ss of exon 5
---------------gtagctattttcatactcgtgtacagatctgagctttgaac------aatttgtacatcagtcactaagttgct-gttctatgccagGACTTTAAGATTCAGAATATTGTTGGCTCTTGTGATGTAAAGTTTCCAATTAGGCTTGAGGGCCTTGCCTATTCTCATGGTGCCTTCTCAAGT
                |   || |||   |   ||| | |   ||    |||  |       |  |||||| | | |   ||| |   | |  |||| ||||||||| ||||||||||| |||||||| ||||||||||| || |||||||| ||||| ||||| ||||| |||||||||||||| |||||||||
gtaactatttcaggcttgattaatttt-catctgtgcaaatgcctaccattttcattctgtaagattgtacctaaatgtttaactcatttgcactataccagGACTTCAAGATTCAGAACATTGTTGGTTCTTGTGATGTTAAATTTCCAATCAGGCTGGAGGGACTTGCATATTCTCATGGTGCTTTCTCAAGT

upper sequence: GRMZM2G149238_T04 (Zea mays), 3'ss of exon 5
lower sequence: LOC_Os03g45410.1 (Oryza sativa), 3'ss of exon 6
----------gtagctattttcatactcgtgtacagatctgagctttgaaca--------atttgtacatcagtcactaagttgctgttctatgccagGACTTTAAGATTCAGAATATTGTTGGCTCTTGTGATGTAAAGTTTCCAATTAGGCTTGAGGGCCTTGCCTATTCTCATGGTGCCTTCTCAAGT
            ||||   || ||  || | |    || ||       || |        | |||||| | | |   ||| |   ||  |||| |||||| || ||||||||||| |||||||||||||||||||| || |||||||| ||||| ||||| ||||| |||||||||||||| |||||||||
gtaactatttcaagcttgcttgattttcatctgtgcatgtgcctaccaaatacattctgtaattgtacctaactgtttaactcattgcactataccagGATTTCAAGATTCAGAACATTGTTGGCTCTTGTGATGTTAAATTTCCAATCAGGCTGGAGGGACTTGCATATTCTCATGGTGCTTTCTCAAGT

upper sequence: GRMZM2G149238_T04 (Zea mays), 3'ss of exon 5
lower sequence: GLYMA16G25450.3 (Glycine max), 3'ss of exon 6
--------------------gtagctattttcatactcgtgtacagatctgagctttgaacaatttgtacatcagtcactaagttgc-tgttctatgccagGACTTTAAGATTCAGAATATTGTTGGCTCTTGTGATGTAAAGTTTCCAATTAGGCTTGAGGGCCTTGCCTATTCTCATGGTGCCTTCTCAAGT
                      | | || ||  |  |  | | |  |    | || ||      |||   |  | |   |   |||  | || |   | |||| || || |||||||| ||||| |||||||||||||| ||||| || ||  |||| ||||| ||||| ||||| |||||||| |||||||||
gtactgcttttgctctttctcaatccatgttttttgttcttttctcactgtaactatgttgtgcttgattactaattggttccttgggtattatgctctagGATTTCAAAATTCAGAACATTGTCGGCTCTTGTGATGTCAAGTTCCCCATACGGCTGGAGGGTCTTGCATATTCCCATGGTGCTTTCTCAAGT

upper sequence: GRMZM2G149238_T04 (Zea mays), 3'ss of exon 5
lower sequence: GLYMA09G41330.2 (Glycine max), 3'ss of exon 5
-----------------gtagctattttcatactcgtgtacagatctg-agctttgaacaat--ttgtacatcagtcactaagttgctgttctatgccagGACTTTAAGATTCAGAATATTGTTGGCTCTTGTGATGTAAAGTTTCCAATTAGGCTTGAGGGCCTTGCCTATTCTCATGGTGCCTTCTCAAGT
                   |   |||||   | | || | |   |||  ||          |  |  |  ||   |  ||   |   | ||||     |||| |||||||||||||| |||||||||||||||||||| ||||| || ||| | |||||||| ||||||||||| |||||||| |||||||||
tttaaggttcaacatctccaaaaattttatcagttgttttccactctacagaagcagtttgtggtcattgatttattcctttttctttattctgctttagGATTTTAAGATTCAGAACATTGTTGGCTCTTGTGATGTCAAGTTCCCCATTCGACTTGAGGGTCTTGCCTATTCCCATGGTGCTTTCTCAAGT

upper sequence: GRMZM2G149238_T04 (Zea mays), 3'ss of exon 5
lower sequence: GLYMA19G28780.1 (Glycine max), 3'ss of exon 6
-----gtagctattttcatactcgtgt--acagatctgagctttgaacaatttgtacatcagtcactaagttgct-----------gttctatgccagGACTTTAAGATTCAGAATATTGTTGGCTCTTGTGATGTAAAGTTTCCAATTAGGCTTGAGGGCCTTGCCTATTCTCATGGTGCCTTCTCAAGT
       | ||| | | | | |  | |     | | |   || |  | || | ||   |  |||| | | ||  |            ||||     |||| |||||||||||||| |||||||||||||||||||| ||||| || ||| | |||||||| ||||||||||| ||| |||| |||||||||
gtacaacatctactctgaaaattttatcagttgttttccactctacagaagtagtttgt-ggtcattgatttattcctttttctttattctgctttagGATTTTAAGATTCAGAACATTGTTGGCTCTTGTGATGTCAAGTTCCCCATTCGACTTGAGGGTCTTGCCTATTCCCATAGTGCTTTCTCAAGT

upper sequence: GRMZM2G149238_T04 (Zea mays), 3'ss of exon 5
lower sequence: GLYMA18G44460.1 (Glycine max), 3'ss of exon 5
------gtagctattttcatactcgtgtacagatctgagctttg----aacaatttgtacatcagtcactaagt--------tgctgttctatgcc--agGACTTTAAGATTCAGAATATTGTTGGCTCTTGTGATGTAAAGTTTCCAATTAGGCTTGAGGGCCTTGCCTATTCTCATGGTGCCTTCTCAAGT
        | |   | | | | | ||     | | |   || |     |  | |||||  |||| | ||| | |        | || || | |||   |||| ||||||||||||||||||||||||||||||||||||||||| || ||| | || ||||| ||||||||||| |||||||| |||||||| 
ggtacaacatccgctctgaaaattgtcagttgttttccactctacagaagtagtttgtg-atcattgacttattccttttttttcttttttgtgctttaGGATTTTAAGATTCAGAATATTGTTGGCTCTTGTGATGTAAAGTTCCCCATTCGACTGGAGGGTCTTGCCTATTCCCATGGTGCTTTCTCAAG-

upper sequence: GRMZM2G149238_T04 (Zea mays), 3'ss of exon 5
lower sequence: GLYMA03G04500.1 (Glycine max), 3'ss of exon 6
---------------------------------------------------------------------------------gtagctattttcatactcgtgtacagatctgagctttgaacaatttgtacatcagtcactaagttgc-tgttctatgccagGACTTTAAGATTCAGAATATTGTTGGCTCTTGTGATGTAAAGTTTCCAATTAGGCTTGAGGGCCTTGCCTATTCTCATGGTGCCTTCTCAAGT
                                                                                   | | |||||  |  |  | | |  |    |  | || |   ||||   |  | |   |   |||  | || |     |||| || || |||||||| ||||| |||||||||||||| ||||| || ||  |||| ||||| ||||| ||||| |||||||| |||||||||
gtactgcttctgctctttctcataatctttgctgaaattattgaaaagcgctattttaaaaattttctattttcccccatttaatccattttggtcgttcttttctcactataattatgtagtgtttgattactaattggttctttgggtattatgctttagGATTTCAAAATTCAGAACATTGTCGGCTCTTGTGATGTCAAGTTCCCCATACGGCTGGAGGGTCTTGCATATTCCCATGGTGCTTTCTCAAGT

upper sequence: GRMZM2G149238_T04 (Zea mays), 3'ss of exon 5
lower sequence: GLYMA02G06370.1 (Glycine max), 3'ss of exon 2
-------------------gtagctattttcatactcgtgtacagatctgagctttgaacaatttgtacatcagtcactaagttgc-tgttctatgccagGACTTTAAGATTCAGAATATTGTTGGCTCTTGTGATGTAAAGTTTCCAATTAGGCTTGAGGGCCTTGCCTATTCTCATGGTGCCTTCTCAAGT
                     | | || ||     |  | | |  |    | || || |   ||||   |  | |   |   |||  | || |     |||| || || |||||||  ||||| |||||||||||||| ||||| || || | ||| ||||| ||||| ||||| |||||||| |||||||||
aatctttgctggaactgtttaatccatgtttgctgttcttttctcactgtaactatgtagtgtttgattactaattggttccttgggtattatgctttagGATTTCAAAATTCAGATCATTGTCGGCTCTTGTGATGTCAAGTTCCCCAT-ATGCTGGAGGGTCTTGCATATTCCCATGGTGCTTTCTCAAGT

upper sequence: GRMZM2G149238_T04 (Zea mays), 3'ss of exon 5
lower sequence: GLYMA09G41330.1 (Glycine max), 3'ss of exon 6
-----------gtagctattttcatactcgtgtacagatctg-agctttgaacaat--ttgtacatcagtcactaagttgctgttctatgccagGACTTTAAGATTCAGAATATTGTTGGCTCTTGTGATGTAAAGTTTCCAATTAGGCTTGAGGGCCTTGCCTATTCTCATGGTGCCTTCTCAAGT
             |   |||||   | | || | |   |||  ||          |  |  |  ||   |  ||   |   | ||||     |||| |||||||||||||| |||||||||||||||||||| ||||| || ||| | |||||||| ||||||||||| |||||||| |||||||||
gttcaacatctccaaaaattttatcagttgttttccactctacagaagcagtttgtggtcattgatttattcctttttctttattctgctttagGATTTTAAGATTCAGAACATTGTTGGCTCTTGTGATGTCAAGTTCCCCATTCGACTTGAGGGTCTTGCCTATTCCCATGGTGCTTTCTCAAGT

upper sequence: GRMZM2G149238_T04 (Zea mays), 3'ss of exon 5
lower sequence: AT3G13445.1 (Arabidopsis thaliana), 3'ss of exon 6
------------gtagctattttcatactcgtgtacagatctgagctttgaacaatttgtacatcagtcactaagttgctgttctatgccagGACTTTAAGATTCAGAATATTGTTGGCTCTTGTGATGTAAAGTTTCCAATTAGGCTTGAGGGCCTTGCCTATTCTCATGGTGCCTTCTCAAGT
              | |  ||| | ||  |    |||  | |   |||        || |||   |   | | | ||| |      ||| |||| || ||||||||||||||||| || ||||||||||| || || || || || ||||| || ||||| || ||||| | ||| |||||||||
gtacaatttctttaaaccttttccctatcca---acattttttttcttacttttgcttatactaaatatattcaattgttacatcctgc-agGATTTCAAGATTCAGAATATTGTAGGTTCTTGTGATGTCAAATTCCCTATAAGACTTGAAGGTCTTGCTTACTCTCACGCTGCTTTCTCAAGT

upper sequence: GRMZM2G149238_T04 (Zea mays), 3'ss of exon 5
lower sequence: AT1G55520.1 (Arabidopsis thaliana), 3'ss of exon 6
--------------------------------------------------gtagctattttcat-----actcgtgtacagatctgagctttgaacaatttgtacat------cagtcactaagttgctgttc---tatgccagGACTTTAAGATTCAGAATATTGTTGGCTCTTGTGATGTAAAGTTTCCAATTAGGCTTGAGGGCCTTGCCTATTCTCATGGTGCCTTCTCAAGT
                                                   |   ||| |  ||     | ||||||  |  | |       | | || ||    ||       ||| |  || |||||| |    | |  ||||| |||||||| ||||| ||||| ||||| |||||||| || || || ||||||||||| || ||||| || |||||| |||| |||||||||
gtactcatatgtctctctctggtcctgatccagcacacactgtgttattcatttttatctcaatcaacaattcgtgtgtatttttatcggaaggaaaaattacgtataaagtctagtaataaaattgctgattacattttgcagGATTTTAAGATACAGAACATTGTAGGCTCATGTGATGTCAAATTCCCCATTAGGCTTGAAGGTCTTGCATACTCTCATAGTGCTTTCTCAAGT

upper sequence: GRMZM2G149238_T04 (Zea mays), 3'ss of exon 5
lower sequence: Vv06s0004g00180.t01 (Vitis vinifera), 3'ss of exon 6
------------------------------------------gtagctattttcatactcgtgtacagatctg---agctttgaacaatttgtacatcagtcactaagtt--gctgttctatgccagGACTTTAAGATTCAGAATATTGTTGGCTCTTGTGATGTAAAGTTTCCAATTAGGCTTGAGGGCCTTGCCTATTCTCATGGTGCCTTCTCAAGT
                                           |  || || |  || || | | |   | |      |  ||  |   || || ||      ||   ||    |||   |||  |||| |||||||||||||| || |||||||| |||||||| || || || || |||||||| |||||||| ||||||||||||||||| || || 
gtatttattccattacatctctctctctctgtgatgtagccaatttctgttatgctattcttctccttgtttttttgccactgttcttattttatattgactgctgttttttattgtgggatgt-agGATTTTAAGATTCAGAACATAGTTGGCTCCTGTGATGTTAAATTCCCCATAAGGCTTGAAGGCCTTGCATATTCTCATGGTGCCTTTTCCAGC

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|78084017|gb|DV512410.1|DV512410
EST:     TATGCTCGTATTATTCAGAAACTTGGTTTTCCAGCTAAATTCAAG                         GACTTTAAGATTCAGAATATTGTTGGCTCTTGTGATGTAAAGTTTCCAATT
genomic: TATGCTCGTATTATTCAGAAACTTGGTTTTCCAGCTAAATTCAAGgtagctattt ... tctatgccagGACTTTAAGATTCAGAATATTGTTGGCTCTTGTGATGTAAAGTTTCCAATT




















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), 49 (downstream exon)
Score: 60

TATGCTCGTATTATTCAGAAACTTGGTTTTCCAGCTAAATTCAAGgtagctattt ... tctatgccagGACTTTAAGATTCAGAATATTGTTGGCTCTTGTGATGTAAAGTTTCCAATTAGGCTTGAGGGCCTTGCCTATTCTCATGGTGCCTTCTCAAGT


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 46

TATGCTCGTATTATTCAGAAACTTGGTTTTCCAGCTAAATTCAAGgtagctattt ... tctatgccagGACTTTAAGATTCAGAATATTGTTGGCTCTTGTGATGTAAAGTTTCCAATTAGGCTTGAGGGCCTTGCCTATTCTCATGGTGCCTTCTCAAGT


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 53

TATGCTCGTATTATTCAGAAACTTGGTTTTCCAGCTAAATTCAAGgtagctattt ... tctatgccagGACTTTAAGATTCAGAATATTGTTGGCTCTTGTGATGTAAAGTTTCCAATTAGGCTTGAGGGCCTTGCCTATTCTCATGGTGCCTTCTCAAGT


Block sizes: 46 (upstream exon), 44 (downstream exon)
Score: 25

TATGCTCGTATTATTCAGAAACTTGGTTTTCCAGCTAAATTCAAGgtagctattt ... tctatgccagGACTTTAAGATTCAGAATATTGTTGGCTCTTGTGATGTAAAGTTTCCAATTAGGCTTGAGGGCCTTGCCTATTCTCATGGTGCCTTCTCAAGT




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gatctgagctttgaacaatttgtacatcagtcactaagttgctgttctatgccagGACTTTAAGATTCAGAATATTGTTGGCTCTTGTGATGTAAAGTTTCCAATTAGGCTTGAGGGCCTTGCCTATTCTCATGGTGCCTTCTCAAGT
                                         ctgttct  CT-rich tract
             aacaattt  TA-rich tract