Sequence
atgc intronic sequence ATGC exonic sequencegtcagttagtatatagttcttatattttgatggttatggatcatacttttgtttgtgctgatgctttcattttggagattgacttctttgaattaattaatcttttcgacattggtacttattaatctaacagATAGAAGTGGGGGATGTACTATGTGAAATTGAAACTGACAAAGCTACACTAGAATTTGAAAGTCTTGAAGAGGG
Basic information
species | Glycine max |
transcript | GLYMA20G33080.1 |
intron # | 6 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA20G33080.1 (Glycine max), 3'ss of exon 6
lower sequence: LOC_Os06g30460.3 (Oryza sativa), 3'ss of exon 5
gtcagttagtatatagttcttatattttgatggttatggatcatacttttgtttgtgctgatgctttcattttggagattgacttctttgaattaattaatcttttcgacattggtacttattaat--ctaacagATAGAAGTGGGGGATGTACTATGTGAAATTGAAACTGACAAAGCTACACTAGAATTTGAAAGTCTTGAAGAGGG
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----gttaggattttgctctgggatatttcataatagaattgaaacatct-----------tgtttccaattcagagttctttatttcttttttatatattagtttcga--tcaaaagttatctgttgtttgcagATAGAAGTTGGTGATGTGATCTGTGAGATAGAAACTGACAAAGCTACGCTTGAGTTTGAGAGCCTTGAAGAGGG
upper sequence: GLYMA20G33080.1 (Glycine max), 3'ss of exon 6
lower sequence: GRMZM2G082664_T01 (Zea mays), 3'ss of exon 7
gtcagttagtatatagttcttatattttgatggt---tatggatcatacttttgtttgtgctgatgctttc---attttggagattgacttctttgaattaattaatcttttcgacattggtacttattaatctaacagATAGAAGTGGGGGATGTACTATGTGAAATTGAAACTGACAAAGCTACACTAGAATTTGAAAGTCTTGAAGAGGG
|| | ||| | |||| |||| | | || | | ||| | || ||| | | |||| |||| | || | | ||| | || | | | ||| |||| | | | |||||||| || || ||||| ||||||| || |||||||| ||||| || || || |||||||| |||||||||||
gttgtgcttttgctagctgttatttttttaaattcaataagaaaaatatcctatttccagcttagggtttcccattttttttgtttaatgtgttttagtt--ctgagaacactatcgttga-actttatgttgttgcagATAGAGGTTGGTGATGTGATATGTGAGATAGAAACTGATAAAGCCACTCTTGAGTTTGAAAGCCTTGAAGAGGG
upper sequence: GLYMA20G33080.1 (Glycine max), 3'ss of exon 6
lower sequence: AT3G52200.1 (Arabidopsis thaliana), 3'ss of exon 10
gtcagttagtatatagttcttatattttgatggttatggatcatacttttgtttgtgctgatgctttcattttggagattgacttctttgaattaattaatcttttcgacattggtacttattaatcta----acagATAGAAGTGGGGGATGTACTATGTGAAATTGAAACTGACAAAGCTACACTAGAATTTGAAAGTCTTGAAGAGGG
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----------------------------gttagtttctggtgac-ccgatgagtaaattggcattgtaatttcaccacaagaaatctgatgtttatgca--cttgcctgtgttgattcttctcatttcatgaaacagATTGAAGTGGGTGATGTCATAGGTGAGATCGAGACTGACAAAGCCACTCTGGAATTTGAAAGCCTTGAAGAGGG
upper sequence: GLYMA20G33080.1 (Glycine max), 3'ss of exon 6
lower sequence: Vv13s0074g00150.t01 (Vitis vinifera), 3'ss of exon 6
gtcagttag---tatatagttcttatattttgatggttatgga----tcatacttttgtttg-------tgctgatgctttcattttggagattgacttctttgaattaattaatcttttcgacattggtactta-----ttaatctaacagATAGAAGTGGGGGATGTACTATGTGAAATTGAAACTGACAAAGCTACACTAGAATTTGAAAGTCTTGAAGAGGG
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gtcagttatattcaaaaagttgatatgatgtgagagtttaaagcttcttaagttccaatttgatataattataaataatgacaataagaaattttcacttgatgagaccatttgttgatttcatctatgaatttggtgatttaatctaacagATTGAGCCAGGTGACGTTCTATGCGAAATAGAGACAGACAAAGCTACCCTTGAGTTTGAAAGTCTTGAAGAGGG
upper sequence: GLYMA20G33080.1 (Glycine max), 3'ss of exon 6
lower sequence: Vv13s0074g00150.t01 (Vitis vinifera), 3'ss of exon 10
gtcagttagtatatagttcttatattttgatggttatggatcatacttttgtttgtgctgatgctttcattttggagattgacttctttgaattaattaatcttttcgaca---ttggt-actta-ttaatctaacagATAGAAGTGGGGGATGTACTATGTGAAATTGAAACTGACAAAGCTACACTAGAATTTGAAAGTCTTGAAGAGGG
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--------gtttgttatgctta---attaaaggttattga----atttcaagtaatattttttttcctgtttggaaaat--acttgttt-atctattcagcctttcctgttctcttgatcatttacttgatctaacagATAGAAGTGGGTGATGTGATATGTGAGATAGAGACAGACAAAGCCACCCTTGAATTTGAAAGTCTTGAAGAGGG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ttgacttctttgaattaattaatcttttcgacattggtacttattaatctaacagATAGAAGTGGGGGATGTACTATGTGAAATTGAAACTGACAAAGCTACACTAGAATTTGAAAGTCTTGAAGAGGG
tattaat putative branch site (score: 2)
ttctttgaattaatta 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtcagttagtatatagttcttatattttgatggttatggatcatacttttgtttgtgctgatgctttcattttggagattgacttctttgaattaattaatcttttcgacattggtacttattaatctaacagATAGAAGTGGGGGATGTACTATGTGAAATTGAAACTGACAAAGCTACACTAGAATTTGAAAGTCTTGAAGAGGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGG