Sequence
atgc intronic sequence ATGC exonic sequence...tcagctaggatgcattgtttctagtgtataattgacttgtccagatcatttgatgatttgaaaaattcatttggttttctattggtccgctgtattaaagTTGTTGGAGACAATCATAAAGAACTGCGGAGATATTGTTCACATGCATGTTGCAGAAAGAGATGTGCTTCATGAGATGGTGAAAATAGTAAAGAAAAAG
Basic information
species | Glycine max |
transcript | GLYMA14G21410.1 |
intron # | 2 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA14G21410.1 (Glycine max), 3'ss of exon 2
lower sequence: LOC_Os01g12880.1 (Oryza sativa), 3'ss of exon 2
tcagctaggatgcattgtttctagtgtataattgacttgtccagatca-tttg---atgatttgaaa--aat--tcatttggttttctattggtccgctgtattaaagTTGTTGGAGACAATCATAAAGAACTGCGGAGATATTGTTCACATGCATGTTGCAGAAAGAGATGTGCTTCATGAGATGGTGAAAATAGTAAAGAAAAAG
| | |||| || | || | | | ||||| || || ||| | ||| | ||| ||| | || |||| | | || ||| | || || | ||||| || || |||||||| || ||||| | ||||||||||||||||||||||||||| | |||||||||||||| ||||| |||||||||
-------tgcttcattattattt-tggagatgtatcttgtttaggacaacttgcacaggatctaaaatgaataatatcctgattttttttgggggagctctgtttcagCTCTTGGAAACTGCAATCAAGAACTGTGGGGATATATTCCACATGCATGTTGCAGAAAGAGATGTGTTGCATGAGATGGTGAAGATAGTGAAGAAAAAG
upper sequence: GLYMA14G21410.1 (Glycine max), 3'ss of exon 2
lower sequence: GRMZM2G062953_T01 (Zea mays), 3'ss of exon 2
tcagctaggatgcat-tgtttctagtgt-ataattgacttgtccagatcatttgatgatt--tgaaaaattcat-ttggttttctattggt-ccgctgtattaaagTTGTTGGAGACAATCATAAAGAACTGCGGAGATATTGTTCACATGCATGTTGCAGAAAGAGATGTGCTTCATGAGATGGTGAAAATAGTAAAGAAAAAG
||| | | | || | | | || ||| | | |||| ||| ||| || ||| || || || | | || |||| || ||||||| || | ||||| || || || ||||| ||||||||||||||||||| |||||| | | ||||| |||||||| ||||| |||||||||
----gtagaacatgtataattttgttatgatgatttttaaatttaa--tatttagctattgccaaaatgttagcattgtcttgctgatgatatctctatatttcagCTGTTGGAAACTGTTATAAAAAATTGTGGGGATATACTTCACATGCATGTTGCAGAGAGAGATATATTGCATGATATGGTGAAGATAGTGAAGAAAAAG
upper sequence: GLYMA14G21410.1 (Glycine max), 3'ss of exon 2
lower sequence: GRMZM2G153138_T02 (Zea mays), 3'ss of exon 2
-tcagctaggatgcattgtttctagtgtataattgacttgtccagatcatttgatgatttgaaaaattcatttggttttctattggt-ccgctgtattaaagTTGTTGGAGACAATCATAAAGAACTGCGGAGATATTGTTCACATGCATGTTGCAGAAAGAGATGTGCTTCATGAGATGGTGAAAATAGTAAAGAAAAAG
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cataacttgtatttaataaggttt-tatatgat-gattattctctatttcgttattatgaaaatattagcattgtctttcagatgacatctctctatttcagTTGTTGGAAACTGTTATTAAAAACTGTGGGGATATACTTCACATGCATGTCGCAGAGAGAGATATATTGCATGAGATGGTGAAGATAGTGAAGAAAAAG
upper sequence: GLYMA14G21410.1 (Glycine max), 3'ss of exon 2
lower sequence: Vv04s0008g03720.t01 (Vitis vinifera), 3'ss of exon 2
tcagctaggatgcattgtttctagtgtataattgacttgtccagatcat-ttgatgatttgaaaaattcatttggttttctattggtccgctgtattaaagTTGTTGGAGACAATCATAAAGAACTGCGGAGATATTGTTCACATGCATGTTGCAGAAAGAGATGTGCTTCATGAGATGGTGAAAATAGTAAAGAAAAAG
| | | ||| | | | || ||| || ||| | | || || | | ||| | |||||||| || ||| | || || || | ||||||||| || |||| ||||| ||||||||||| || |||||||| ||||| |||||| | |||||||||||||||||||||||||||||||||
ccttcagttgtagatttcattcaatcaattgttgcattctcctgcttgcctttatctgatagaggattaaattggttttgcttttgtct-ttctactatagCTATTGGAGACAGTCGTAAAAAACTGTGGAGATATTGTCCATATGCATGTAGCAGAGAGAGATATTCTTCATGAGATGGTGAAAATAGTAAAGAAAAAG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tcatttgatgatttgaaaaattcatttggttttctattggtccgctgtattaaagTTGTTGGAGACAATCATAAAGAACTGCGGAGATATTGTTCACATGCATGTTGCAGAAAGAGATGTGCTTCATGAGATGGTGAAAATAGTAAAGAAAAAG
atttgat putative branch site (score: 5)
atttgaaaaattcatt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
tcagctaggatgcattgtttctagtgtataattgacttgtccagatcatttgatgatttgaaaaattcatttggttttctattggtccgctgtattaaagTTGTTGGAGACAATCATAAAGAACTGCGGAGATATTGTTCACATGCATGTTGCAGAAAGAGATGTGCTTCATGAGATGGTGAAAATAGTAAAGAAAAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAA
- - - -ggatgca
- - - - - - - - - - - - - - - - tgacttg
- - - - - - - - - - - - - - - - - - - - - - - - - - -tgatttg