Sequence
atgc intronic sequence ATGC exonic sequence...gtgttaggctacaaacatgatgtggtattttttattgatttacgatccattagtttcaaatcaacaaagatttgtgttattcactatagtatacatacagGATGCTGTGGAGTATGCTGAATGTGAAGCTGCTGTGAAAGATTTCCCTCCATTTCGTGAAGCAATGAAGAGAAGAGGGATAGAGGACATGGATCTTGTGA
Basic information
species | Glycine max |
transcript | GLYMA02G04360.1 |
intron # | 3 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA02G04360.1 (Glycine max), 3'ss of exon 3
lower sequence: LOC_Os04g40040.1 (Oryza sativa), 3'ss of exon 4
gtgttaggctacaaacatgatgtggtattttttattgatttacgatccattagtttcaaatcaacaaagatttgtgttattcactatagtatacat-acagGATGCTGTGGAGTATGCTGAATGTGAAGCTGCTGTGAAAGATTTCCCTCCATTTCGTGAAGCAATGAAGAGAAGAGGGATAGAGGACATGGATCTTGTGA
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-tttccgatatttatgcttgtattacagcttgaactgttttttcttttgaagttttttagaaccttttggagcgctcagttcaaatttctatatttcacagGATGCTATGGAGTATGCTGAATGTGAAGCTACTGTCAAAAGCTATCCTCCATTTATTGAAGCTATGAAGAGAAGAGGTGTAGATGACATGGAACTTGTCA
upper sequence: GLYMA02G04360.1 (Glycine max), 3'ss of exon 3
lower sequence: LOC_Os02g38010.1 (Oryza sativa), 3'ss of exon 3
-gtgttaggctacaaacatgatgtggtattttttattgatttacgatccattagtttcaaatcaacaa--agatttgtgttatt-cactatagtatacatacagGATGCTGTGGAGTATGCTGAATGTGAAGCTGCTGTGAAAGATTTCCCTCCATTTCGTGAAGCAATGAAGAGAAGAGGGATAGAGGACATGGATCTTGTGA
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gaaacttagtttgatgcttactttgatagtt---aagcacttagtgaatacttatattaggtcaattactagatttatcttgtagtgcttgtgtgtat-tacagGATGCCATGGAATATGCTGAATGTGAAGCTACTGTGAAAAGTCACCCCCCTTTCATTGAAGCAATGAAAAAAAGAGGAGTTGATGACATGGATCTTGTCA
upper sequence: GLYMA02G04360.1 (Glycine max), 3'ss of exon 3
lower sequence: GRMZM2G147884_T01 (Zea mays), 3'ss of exon 3
-----gtgttaggctacaaacatgatgtgg-tattttttattgatttacgatccattagtttcaaatcaacaaagatttgtgttattcactatagtatacatacagGATGCTGTGGAGTATGCTGAATGTGAAGCTGCTGTGAAAGATTTCCCTCCATTTCGTGAAGCAATGAAGAGAAGAGGGATAGAGGACATGGATCTTGTGA
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aatttatggaagctatgagaagtggtgtggatggcatggatcgtgttac--tcaactattttaaaattttatctgctatttatttttttttatctttgaca----gGATGCTATGGAGTATGCTGAATGTGAGGCTACTGTCAAAAGTTATCCTCCATTTATTGAAGCTATGAAGAGAAGAGGTGTGGATGACATGGATCTTGTTA
upper sequence: GLYMA02G04360.1 (Glycine max), 3'ss of exon 3
lower sequence: Vv00s0225g00090.t01 (Vitis vinifera), 3'ss of exon 3
----gtgttaggctacaaacatgatgtggtattttttattgatttacgatccattagtttcaaatcaacaaagatttgtgttattcactatagtatacatacagGATGCTGTGGAGTATGCTGAATGTGAAGCTGCTGTGAAAGATTTCCCTCCATTTCGTGAAGCAATGAAGAGAAGAGGGATAGAGGACATGGATCTTGTGA
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cttcttattcccttccttacaagcacttctagttcctagtaaat-aagttctatatgcttttgtttaacatccatttccttccttgactttgcaatg---atagGATGCTGTAGAATATGCTGAATGTGAAGCTGTTGTAAAGGATTTTCCTCCATTTCGGGAGGCAATGAAGAAAAGGGGTATTGAGGATATGGATCTTGTGA
upper sequence: GLYMA02G04360.1 (Glycine max), 3'ss of exon 3
lower sequence: PP1S9_129V6.1 (Physcomitrella patens), 3'ss of exon 3
------------------------------------------------------------------------gtgttaggctacaaacatgatgtggtattttttattg---atttacgatc--cattagtttcaaatcaacaaagatttgtgttattcactatagtatacatacagGATGCTGTGGAGTATGCTGAATGTGAAGCTGCTGTGAAAGATTTCCCTCCATTTCGTGAAGCAATGAAGAGAAGAGGGATAGAGGACATGGATCTTGTGA
| || | | || || | | | || || || | | | | || || | || | |||| || | || || || | | |||||||||||||||||||||||||||||||| ||| ||||| || | |||||| ||||| ||||| ||||| | |||||||||||||| |
gtacttttgctctacttctacattagccgattaatttactaaacgattgagtgattggttgattcttatctaatcttgtgacaagtacttgcggcgcagatcttcgatgcctatgtcctaccaatatgagagttaattttgcaaatgatttt-ttcttgtctgtgttgggatggcagGATGCTGTGGAGTATGCTGAATGTGAAGCACTTGTAAAAGAGCATCCAGCTGCCATTGAAGCCATGAAAAGAAGGGGGATTTACGACATGGATCTTGTTA
upper sequence: GLYMA02G04360.1 (Glycine max), 3'ss of exon 3
lower sequence: PP1S178_54V6.1 (Physcomitrella patens), 3'ss of exon 3
--------------------------------------gtgttaggctacaaacatgatgtggtattttttat---tgatttacgatccattagtttcaaatcaacaaa-gatttgtgttattcactatagtatacatacagGATGCTGTGGAGTATGCTGAATGTGAAGCTGCTGTGAAAGATTTCCCTCCATTTCGTGAAGCAATGAAGAGAAGAGGGATAGAGGACATGGATCTTGTGA
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gtaggggtgctaagtctctgtagtagtcgttagttttctcatttactaggtggcacgaagttaattctttgagaagtgcctgtgggggcttttatcactgttctgtaagtgacttttacaattcg---tgctgcgctgtcagGATGCTGTGGAGTATGCTGAATGTGAAGCAACTGTGAAAGAGCATCCGTCTTTCGTTGAAGCCATGAAGAAACGGGGTATCGAGGATATGGATCTTGTGA atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tccattagtttcaaatcaacaaagatttgtgttattcactatagtatacatacagGATGCTGTGGAGTATGCTGAATGTGAAGCTGCTGTGAAAGATTTCCCTCCATTTCGTGAAGCAATGAAGAGAAGAGGGATAGAGGACATGGATCTTGTGA
tatagtata 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtgttaggctacaaacatgatgtggtattttttattgatttacgatccattagtttcaaatcaacaaagatttgtgttattcactatagtatacatacagGATGCTGTGGAGTATGCTGAATGTGAAGCTGCTGTGAAAGATTTCCCTCCATTTCGTGAAGCAATGAAGAGAAGAGGGATAGAGGACATGGATCTTGTGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CATGGA
- - - - - -caaacat
- - - - - - - - - gatgtgg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - -atcaaca
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tttgtgt