Sequence
atgc intronic sequence ATGC exonic sequencegtatgtaataactaataaatgcactataccatctaatttgtagttgcatatcatgcatggttgagttaatatttgtggacgtgttgttcagATAAGCGATGGATGTCAATGGAGGAAATATGGACAAAAGATGGCCAAGGGTAACCCTTGCCCTCGTGCCTACTATCGATGCACCATGGCCGCTGGATGCC
Basic information
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: Vv07s0005g02570.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: LOC_Os05g04640.1 (Oryza sativa), 3'ss of exon 4
---gtatgtaataactaataaatgcactata------ccatctaatttgtagtt-gcatatcatgcatggttgagttaatatttgtggacgtgttgttcagATAAGCGATGGATGTCAATGGAGGAAATATGGACAAAAGATGGCCAAGGGTAACCCTTGCCCTCGTGCCTACTATCGATGCACCATGGCCGCTGGATGCC
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catgcaccatatagctgatgaaaaaactgaaagttatatatatgctttataatcagtaattaaattaactttaagcatatatacatgtttatat-atgtagATCAGTGATGGATGCCAATGGAGGAAGTACGGGCAGAAGATGGCCAAGGGTAACCCTTGCCCTAGAGCCTACTACCGATGCACAATGGCTTCGCAATGCC
upper sequence: Vv07s0005g02570.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: GRMZM2G327349_T01 (Zea mays), 3'ss of exon 4
--------gtatgtaataactaata-aatgcactataccatctaatttgta-gttgcatatcatgcatggttgagttaatatttgtggacgtgttgttcagATAAGCGATGGATGTCAATGGAGGAAATATGGACAAAAGATGGCCAAGGGTAACCCTTGCCCTCGTGCCTACTATCGATGCACCATGGCCGCTGGATGCC
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ctctccgcacatatagttattccaataatacacatagtgatgtacatagtccgtcctgcaattgcaatgtatatgacattattattttgcctaac-tgtagATTAGCGACGGGTGTCAATGGCGGAAGTACGGGCAGAAGATGGCCAAAGGTAACCCATGCCCGAGAGCATACTATCGGTGCACAATGGCTGTGGCATGCC
upper sequence: Vv07s0005g02570.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: GLYMA19G40950.1 (Glycine max), 3'ss of exon 6
------gtatgtaataactaataaatgcactat-accatctaatttgtagttgcatatca--tgcatggttgagttaatatttgtggacgtg--ttgttcagATAAGCGATGGATGTCAATGGAGGAAATATGGACAAAAGATGGCCAAGGGTAACCCTTGCCCTCGTGCCTACTATCGATGCACCATGGCCGCTGGATGCC
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aataccatatacaataagaaa-aattccattgttagcatcttgtccaacaacacacagtaattgaatgaacaa-ttaatgttcgatgctatggccctttcagATAAGCGATGGATGTCAGTGGAGGAAATATGGACAAAAAATGGCCAAGGGTAACCCTTGCCCTCGTGCTTACTATCGCTGCACTATGGCTGTAGGATGCC
upper sequence: Vv07s0005g02570.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: GLYMA03G38360.1 (Glycine max), 3'ss of exon 4
gtatgtaat--aactaata-aatgcacta-taccatcta-atttgtagttgcatatcatgcatggttga---gttaatatttgtggacgtg--ttgttcagATAAGCGATGGATGTCAATGGAGGAAATATGGACAAAAGATGGCCAAGGGTAACCCTTGCCCTCGTGCCTACTATCGATGCACCATGGCCGCTGGATGCC
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-ttcttaattcaactagtttaatgcccgggtagcaaatggatgcatacatgtagaaattaattgaatgaacaattaacgttttgtgctgtggccctttcagATTAGCGATGGATGTCAGTGGAGGAAATATGGACAAAAAATGGCCAAGGGTAACCCTTGCCCTCGTGCTTACTATCGCTGCACTATGGCTGTAGGATGCC
upper sequence: Vv07s0005g02570.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: GLYMA10G27860.1 (Glycine max), 3'ss of exon 7
gtatgtaataa--ctaataaatgcactata---ccatctaatttgtagttgcatatc-atgcatggttgagt-taatatttgtggacgtgt-----tgttcagATAAGCGATGGATGTCAATGGAGGAAATATGGACAAAAGATGGCCAAGGGTAACCCTTGCCCTCGTGCCTACTATCGATGCACCATGGCCGCTGGATGCC
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--atataataaggctacctaattaaatataaatttccccagttaaaatctactaatccacgcatatttttgtgtaatata-atgaatgtgcattaattttcagATTAGCGATGGATGTCAATGGAGGAAATATGGACAAAAAATAGCCAAGGGTAATCCTTGTCCCCGTGCCTATTATCGTTGCACTATGGCCGTAGGATGCC
upper sequence: Vv07s0005g02570.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: GLYMA02G01030.1 (Glycine max), 3'ss of exon 2
--------------------------------------------------------------------gtatgtaataactaataaatgcactataccatctaatttgtagttgcatatcatgcatggttgagttaatatttgtggacgtgttgttcagATAAGCGATGGATGTCAATGGAGGAAATATGGACAAAAGATGGCCAAGGGTAACCCTTGCCCTCGTGCCTACTATCGATGCACCATGGCCGCTGGATGCC
||| ||| || | | | | ||| | | || | ||| || | | ||| |||| | || ||||||| || |||||||||||||||||||||||||||||||| || ||||||||||| ||||| || |||||||| ||||| ||||| ||||||| |||||||
gtaatgattaaatttattttaattatatgtcttaatttatactattgcatattatgtaaattgatataacgctacttaattaaataaaaatttctccagttaaatctactaatccaca-catttatatgtatat-aatgaatgtgcattaatt-ttcagATTAGTGATGGATGTCAATGGAGGAAATATGGACAAAAAATAGCCAAGGGTAATCCTTGTCCCCGTGCCTATTATCGTTGCACTATGGCCGTAGGATGCC
upper sequence: Vv07s0005g02570.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: AT4G01720.1 (Arabidopsis thaliana), 3'ss of exon 4
----gtatgtaataactaataaatgcactataccatctaat-ttgtagttgcatatcatgcatgg---ttgagttaatatttgtggacgtgttgttcagATAAGCGATGGATGTCAATGGAGGAAATATGGACAAAAGATGGCCAAGGGTAACCCTTGCCCTCGTGCCTACTATCGATGCACCATGGCCGCTGGATGCC
| | || | || ||| | | | | ||| || | | |||| | ||| |||| | |||||| | | | | || ||| || |||||||||||||| ||||| || || || ||||| || || || || || ||||| || || ||||| ||||||||||||| |||||| |
gtaactttctataagttactaatttttttgattcgtttaaccttacatatatatatgagttatgaaaattgaatcaatatt----aatatataatatagGTAAATGACGGATGTCAATGGAGAAAATACGGTCAGAAAATGGCGAAAGGGAATCCATGTCCTCGCGCTTATTATCGTTGCACCATGGCCGTTGGATGTC
upper sequence: Vv07s0005g02570.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: PP1S47_251V6.1 (Physcomitrella patens), 3'ss of exon 3
----------------------------------gtatgtaataactaataaatgcactataccatctaatttgtagttgcatatcatgcatggt---tgagttaatatttgtggacgtgttgttcagATAAGCGATGGATGTCAATGGAGGAAATATGGACAAAAGATGGCCAAGGGTAACCCTTGCCCTCGTGCCTACTATCGATGCACCATGGCCGCTGGATGCC
| | | | | | | | || | | || | ||| | | | | ||| | | || | | || |||| | || ||||| || |||||||||||||| || |||||||| || || ||||| || |||||||| ||||| ||||||||| | || | || || |
gtacgttcctgtccttttcatagaacccttctctacacgcttttaaaattcagcaccggattcagtgcttttcatcgttaaggtttaatcgggtcccatgatctcacatgatgatttatctgttttagATCAATGACGGATGCCAGTGGAGGAAATATGGTCAGAAGATGGCGAAAGGGAACCCCTGTCCTCGTGCATACTACCGATGCACCGTTGCGCCGGGCTGTC atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tttgtagttgcatatcatgcatggttgagttaatatttgtggacgtgttgttcagATAAGCGATGGATGTCAATGGAGGAAATATGGACAAAAGATGGCCAAGGGTAACCCTTGCCCTCGTGCCTACTATCGATGCACCATGGCCGCTGGATGCC
agttaat putative branch site (score: 4)
ttgagttaatattt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtatgtaataactaataaatgcactataccatctaatttgtagttgcatatcatgcatggttgagttaatatttgtggacgtgttgttcagATAAGCGATGGATGTCAATGGAGGAAATATGGACAAAAGATGGCCAAGGGTAACCCTTGCCCTCGTGCCTACTATCGATGCACCATGGCCGCTGGATGCC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGGA