Sequence
atgc intronic sequence ATGC exonic sequencegtcagttagcaactatacatatccatatcaaatgttttgtttttatttagctcaaaatgtctttttttttttaatggatgattgcagttttttatttttattttttggggattgagggtttctgagaatttgtttatttctgaattccacccacgtgtttatttcggcgtgcagGGCGAGTGAGAAATGCCAGAAGGAGAAGAGAAAGACAATCAATGGAGACGATTTGCTATGGGCCATGGCCACTTTAGGATTTGAAGACTACATAGAGCCG
Basic information
species | Glycine max |
transcript | GLYMA20G34050.1 |
intron # | 1 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA20G34050.1 (Glycine max), 3'ss of exon 1
lower sequence: GRMZM2G303465_T04 (Zea mays), 3'ss of exon 1
gtcagttagcaactatacatatccatatcaaatgttttgtttttatttagctcaaaatgtctttttttttttaatggatgattgcagttttttatttttattttttggggattgagggtttctgagaatttgtttatttctgaattccacccacgtgtttattt-cggcgtgcagGGCGAGTGAGAAATGCCAGAAGGAGAAGAGAAAGACAATCAATGGAGACGATTTGCTATGGGCCATGGCCACTTTAGGATTTGAAGACTACATAGAGCCG
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---------------------------------------------gtaagttgacagt---tggcaccgcctggtagacggtagcgtagcgtagccttggtcttggatcgggttggtttttctttgttttaatgtaggataggttctgatgtaagttcacgggtgctggttgcagGGCCAGCGACAAATGCCAGAAGGAGAAACGAAAGACAATCAACGGGGACGATTTGCTCTGGGCGATGGCCACTTTAGGATTCGAGGAGTACGTCGAGCCT
upper sequence: GLYMA20G34050.1 (Glycine max), 3'ss of exon 1
lower sequence: GRMZM5G804893_T01 (Zea mays), 3'ss of exon 2
gtcagttagcaactatacatatccatatcaaatgttttgtttttattt-agctcaaaatgtctttttttttttaatggatgattgcagttttttatttttattttttggggattgagggtttctgagaatttgtttatttctgaattccacccacgtgtttatttcggcg---tgcagGGCGAGTGAGAAATGCCAGAAGGAGAAGAGAAAGACAATCAATGGAGACGATTTGCTATGGGCCATGGCCACTTTAGGATTTGAAGACTACATAGAGCCG
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--------------------------------------gtaagtgcctcagctgcggctgactcttacttttgcttggcttgttgggaatttggagtggcgttc---agggctttagcttggctggggttttgtgt-tgacttgtccatgtccacgtttttttgtccgctctttgcagAGCGAGTGACAAGTGCCAGAGGGAGAAGCGGAAGACCATCAATGGCGACGATCTGCTGTGGGCCATGGCCACGCTGGGGTTTGAAGACTACATTGAACCC
upper sequence: GLYMA20G34050.1 (Glycine max), 3'ss of exon 1
lower sequence: GRMZM2G064426_T02 (Zea mays), 3'ss of exon 2
gtcagttagcaactatacatatccatatcaaatgttttgtttttatttagctcaaaatgtctttttttttttaatggatgattgcagttttttatttttattttttggggattgagggtttctgagaatttgtttatttctgaattccacccacgtgtttatttcggcgtgcagGGCGAGTGAGAAATGCCAGAAGGAGAAGAGAAAGACAATCAATGGAGACGATTTGCTATGGGCCATGGCCACTTTAGGATTTGAAGACTACATAGAGCCG
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--------gtaagtcc-ctcggccgcggctgactctgactcttctgtttgcttggcatgt--------tgggaattcagagtggcgtttcgcaaaccgcactttagcttaggtggggttttgtgttgacttgtctacgtccacgttcct------tgtctgct---gtttgcagGGCGAGTGACAAGTGCCAGAGGGAGAAGCGGAAGACCATCAATGGCGACGACCTGCTGTGGGCCATGGCCACGCTGGGGTTTGAGGACTATATTGAACCC
upper sequence: GLYMA20G34050.1 (Glycine max), 3'ss of exon 1
lower sequence: Vv13s0019g03600.t01 (Vitis vinifera), 3'ss of exon 2
gtcagttagcaactatacatatccatatcaaatgttttgtttttatttagctcaaaatgtctttttttttttaatggatgattgcagttttttatttttattttttggggattgagggtttctgagaatttgtttatttctgaattccacccacgtgtttatttcggcgtgcagGGCGAGTGAGAAATGCCAGAAGGAGAAGAGAAAGACAATCAATGGAGACGATTTGCTATGGGCCATGGCCACTTTAGGATTTGAAGACTACATAGAGCCG
||||| || || | | || |||| | ||| |||| || | | ||||||| | ||| ||| | ||| | | | | | | ||||| ||||| || || ||||| |||||| ||||||| || ||||| || ||| |||| ||||| ||||| || ||||||||||||| || || || ||
-----------------------------------------------------aaaatatccttcacct--------aacatggcag------agtttgatttacaaggaaattagggttttgg----ttttgcaattgcaaaatattttttgaaaatgtttcttg---tttagGGCTAGTGATAAGTGTCAGAAAGAGAAGCGAAAGACGATTAATGGTGATGATCTGCTTTGGGCGATGGCGACCCTAGGATTTGAAGATTATATTGAACCA
upper sequence: GLYMA20G34050.1 (Glycine max), 3'ss of exon 1
lower sequence: PP1S25_89V6.1 (Physcomitrella patens), 3'ss of exon 2
gtcagttagcaactatacatatccatatcaaatgttttgtttttatttagctcaaaatgtctttttttttttaatggatgattgcagttttttatttttattttttggggattgagggtttctgagaatttgtttatttctgaattccacccacgtgtttatttcggcgtg---cagGGCGAGTGAGAAATGCCAGAAGGAGAAGAGAAAGACAATCAATGGAGACGATTTGCTATGGGCCATGGCCACTTTAGGATTTGAAGACTACATAGAGCCG
|||| || | || | || | || | | ||| | | | | | | | | | | | | |||| | | | | ||| || || || || || ||| ||| ||||||||||| ||||||||||| ||||| || ||||||||| ||| ||||| |||||||||||| | ||||||
---------------------------------------------------------------------------tgatggtttct-ttgatcatgtgtacaatgtaaaacttggcgttatttttgtttgtcctccctgcaccgcattgtctgc-cgttttccttgacctattacagAGCTAGCGACAAGTGTCAGCGGGAAAAGAGAAAGACGATCAATGGAGATGATTTACTTTGGGCCATGAGCACATTAGGGTTTGAAGACTACGTCGAGCCG
upper sequence: GLYMA20G34050.1 (Glycine max), 3'ss of exon 1
lower sequence: PP1S25_10V6.1 (Physcomitrella patens), 3'ss of exon 2
gtcagttagcaactatacatatccatatcaaatgttttgtttttatttagctcaaaatgtctttttttttttaatggatgattgcagttttttatttttattttttggggattgagggtttctgagaatttgtttatttctgaattccacccacgtgtttatttcggcgtgcagGGCGAGTGAGAAATGCCAGAAGGAGAAGAGAAAGACAATCAATGGAGACGATTTGCTATGGGCCATGGCCACTTTAGGATTTGAAGACTACATAGAGCCG
|| || || || || |||| | | || | | | || |||||| || | || || | || | || | | || || ||| || || || ||||| ||| || |||||||||||||| |||||||||||||| || ||||| ||| ||| ||||| || ||||||||| | || |||
-----------------------------------------------------------tcaccttagttcta--ggtgtattggattcttagg---tcacgtacaggatgttgagg-----tggaagttctttggcatttgtctgtcattttccttgacatatca-----cagAGCTAGCGACAAATGTCAGCGCGAAAAGAGAAAGACAATAAATGGAGACGATTTACTGTGGGCTATGAGCACATTAGGGTTCGAAGACTACGTCGAACCG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ttctgagaatttgtttatttctgaattccacccacgtgtttatttcggcgtgcagGGCGAGTGAGAAATGCCAGAAGGAGAAGAGAAAGACAATCAATGGAGACGATTTGCTATGGGCCATGGCCACTTTAGGATTTGAAGACTACATAGAGCCG
tttatttc CT-rich tract
agaatttgtttattt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtcagttagcaactatacatatccatatcaaatgttttgtttttatttagctcaaaatgtctttttttttttaatggatgattgcagttttttatttttattttttggggattgagggtttctgagaatttgtttatttctgaattccacccacgtgtttatttcggcgtgcagGGCGAGTGAGAAATGCCAGAAGGAGAAGAGAAAGACAATCAATGGAGACGATTTGCTATGGGCCATGGCCACTTTAGGATTTGAAGACTACATAGAGCCG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGA