Sequence
atgc intronic sequence ATGC exonic sequencegtactcttcttctggcatttgattcgaggtttattttggtttggttgctgagaattgtttgattagcttttcagcgaccttttatgtgatttgtatttctctgcaaccaagcatggcagagttttacaactttttggcggcttaaactgatttgttttcgtaatatttgaacagCGAAAGCTTGCGCAAAGATCAGAGAGAGTAAAGTCTGTGGATCTACATCCAACAGAACCATG
Basic information
species | Glycine max |
transcript | GLYMA07G03890.1 |
intron # | 2 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA07G03890.1 (Glycine max), 3'ss of exon 2
lower sequence: AT1G52360.1 (Arabidopsis thaliana), 3'ss of exon 2
gtactcttcttctggcatttgattcgaggtttattttggtttggttgctgagaattgt-ttgattagcttttcagcgaccttttatgtgatttgtatttctctgcaaccaagcatggcagagttttacaactttttggcggcttaaactgatttgttttcgtaatatttgaa-cagCGAAAGCTTGCGCAAAGATCAGAGAGAGTAAAGTCTGTGGATCTACATCCAACAGAACCATG
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--------------------------------------------------------gtattgtttcgatttccatttagtttttttgagggatttctttttatgtcat------tcgctctgtttt-----tttttcgctgtgttga-taatttctttgcgttgtttttggttcagAGAAAATTAGCGCAAAGGTCTGAGAGAGTTAAATCTGTGGATCTTCATCCTACAGAACCATG
upper sequence: GLYMA07G03890.1 (Glycine max), 3'ss of exon 2
lower sequence: AT1G79990.1 (Arabidopsis thaliana), 3'ss of exon 6
gtactcttcttctggcatttgattcgaggtttattttggtttggttgctgagaattgtttgattagcttttcagcgaccttttatgtgatttgtatttctctgcaaccaagcatggcagagttttacaactttttggcggcttaaactgatttgttttcgtaatatttgaacagCGAAAGCTTGCGCAAAGATCAGAGAGAGTAAAGTCTGTGGATCTACATCCAACAGAACCATG
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-------------------------------------------------------------------------------------gtaatgcagtctcctttgatgctcgattt--catccttaatcattcttattcgggactgtattgacacgcttctttgt--tttgatcagCGTAAGTTTGCTCAAAGATCAGAAAGAGTCAAATCTGTAGATCTCCATCCAACAGAGCCATG
upper sequence: GLYMA07G03890.1 (Glycine max), 3'ss of exon 2
lower sequence: AT3G15980.3 (Arabidopsis thaliana), 3'ss of exon 2
gtactcttcttctggcatttgattcgaggtttattttggtttggttgctgagaattgtttgattagcttttcagcgaccttttatgtgatttgtatttctctgcaaccaagcatggcagagttttacaactttttggcggcttaaactgatttgttttcgtaatattt-gaacagCGAAAGCTTGCGCAAAGATCAGAGAGAGTAAAGTCTGTGGATCTACATCCAACAGAACCATG
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-------------------------------------------------------------------------------------gtattgcttatctttcaactttctgcttctgtta--ttttatta--ttatagctg-tggtcataatttgcttttgttatgttttgatcagAGAAAGTTTGCTCAACGATCAGAGAGAGTCAAATCTGTTGATCTGCATCCTACTGAACCATG
upper sequence: GLYMA07G03890.1 (Glycine max), 3'ss of exon 2
lower sequence: Vv11s0016g04180.t01 (Vitis vinifera), 3'ss of exon 2
gtactcttcttctggcatttgattcgaggtttattttggtttggttgctgagaattgtttgattagcttttcagcgaccttttatgtgatttgtatttctctgcaaccaagcatggcagagttttacaactttttggcggcttaaactgatttgttttcgtaatatttgaacagCGAAAGCTTGCGCAAAGATCAGAGAGAGTAAAGTCTGTGGATCTACATCCAACAGAACCATG
||||| ||| || | || | | |||| | | | ||| || |||||| | | | | | | | || | | ||| ||| | | ||| |||| || ||| |||| ||||| |||||||| || |||||||| || ||||||||||||||||| ||||||||
------------------------------gtatttatgttcatccacttgaatttatcttgttaggct---aataaatgtttccatgctttgtaatccagttatatctttagttttcaaaagttgtagcgttt----agctaacaatgacctgtt------------gatcagAGAAAACTTGCACAAAGATCTGAAAGAGTAAAATCAGTGGATCTACATCCAACTGAACCATG
upper sequence: GLYMA07G03890.1 (Glycine max), 3'ss of exon 2
lower sequence: Vv09s0002g04810.t01 (Vitis vinifera), 3'ss of exon 2
gtactcttcttctggcatttgattcgaggtttattttggtttggttgctgagaattgtttgattagcttttcagcgaccttttatgtgatttgtatttctctgc--aaccaagcatggcagagttttacaactttttggcggcttaaactgatttgttttcgtaatattt--gaacagCGAAAGCTTGCGCAAAGATCAGAGAGAGTAAAGTCTGTGGATCTACATCCAACAGAACCATG
| |||| | ||||| | |||||| ||| | | | | | | | | || || || | | |||| || | | |||| || ||| | || || ||||||||||||||||||||||| ||||||||||| |||||| | || |||||
-------------------------------------------------------------gtacgcttgtttattccctttgaattgatttctatgtacagattagatctcgatttgtttaatgtt-taatagttgaagtattgatgtcattttgcttctggtaaattttggatcagAGGAAACTCGCGCAAAGATCAGAGAGAGTAAAATCTGTGGATCTGCATCCATCTGAGCCATG
upper sequence: GLYMA07G03890.1 (Glycine max), 3'ss of exon 2
lower sequence: PP1S79_180V6.1 (Physcomitrella patens), 3'ss of exon 2
gtactcttcttctggcatttgattcgaggtttattttggtttggttgctgagaattgtttgattagcttttcagcgaccttttat-gtgatttgtatttctctgcaaccaagcatggcagagttttacaactttttggcggcttaaactgatttgttttcgtaatatttgaacagCGAAAGCTTGCGCAAAGATCAGAGAGAGTAAAGTCTGTGGATCTACATCCAACAGAACCATG
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-----------------------------------------------------------------------aattgaattcttctcatcatcagcagtgttgcagagtgtgaagtggtga--ttttatgcctgcacag-gttttgtgctgata-gtgctgattttcttatttcagCGGAAACTCGCGCAAAGGTCTGAGCGAGTTAAGTGTGTGGATCTTCATCCAACAGAGCCATG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.agttttacaactttttggcggcttaaactgatttgttttcgtaatatttgaacagCGAAAGCTTGCGCAAAGATCAGAGAGAGTAAAGTCTGTGGATCTACATCCAACAGAACCATG
aactgat putative branch site (score: 3)
ttttcgtaatattt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtactcttcttctggcatttgattcgaggtttattttggtttggttgctgagaattgtttgattagcttttcagcgaccttttatgtgatttgtatttctctgcaaccaagcatggcagagttttacaactttttggcggcttaaactgatttgttttcgtaatatttgaacagCGAAAGCTTGCGCAAAGATCAGAGAGAGTAAAGTCTGTGGATCTACATCCAACAGAACCATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGATCA