Sequence
atgc intronic sequence ATGC exonic sequencegttagtaacaatgctattattattttcccttaccatattgtctacttattcccaaatctatatataatcttcaaaaatcatcttgacaaatatattctgtgcattgcagGTTGTGCCACCGGATCAAGCTCGGAAAATATACCAGGCGGTGAAAGAAAAAGGTGTGCCAGTTGCTCTTGTTGAGTATGAAGGAGAACAACACGGTTTCC
Basic information
species | Glycine max |
transcript | GLYMA18G11480.1 |
intron # | 16 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA18G11480.1 (Glycine max), 3'ss of exon 16
lower sequence: GRMZM2G120302_T02 (Zea mays), 3'ss of exon 16
---gttagtaacaatgctattattattttcccttaccatattgtctacttattcccaaatctatatataatcttcaaaaatcatcttgacaaatatattctgtgcattgcagGTTGTGCCACCGGATCAAGCTCGGAAAATATACCAGGCGGTGAAAGAAAAAGGTGTGCCAGTTGCTCTTGTTGAGTATGAAGGAGAACAACACGGTTTCC
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gtatttgctgaccatga-actgtaaagtt----tatcatg--gctccattactcagtggtatatcgatgttttctatagcataatttgtcacctgc-tttaacgttttctagGTTGTGCCACCAGATCAGGCACGCAAAATATACAGTGCCTTGAAAGAGAAAGGTTTGCCTGTTGCTTTGGTTGAATATGAAGGAGAGCAGCATGGGTTCC
upper sequence: GLYMA18G11480.1 (Glycine max), 3'ss of exon 16
lower sequence: AT5G36210.1 (Arabidopsis thaliana), 3'ss of exon 16
gttagtaacaatgctattattattttcccttaccatattgtctacttattcccaaatctatatataatcttcaaaaatcatcttgacaaatatattctgtgcattgcagGTTGTGCCACCGGATCAAGCTCGGAAAATATACCAGGCGGTGAAAGAAAAAGGTGTGCCAGTTGCTCTTGTTGAGTATGAAGGAGAACAACACGGTTTCC
|| ||| | ||| | || ||| || | | | | | | || | | |||||| ||| | || || || || || | |||||||||||| | || |||||| | || ||||| || | || | || |||||||| |||| ||||||||||| ||||| |||||||||||||||||||| |
-tttttaaattcgagatt-tggttatccatttgcgaa--gacaatgtctttc-acttctatacgaaattcttaacgattggttt----aaaatgctgaaaaaattgcagGTTGTAACTCCAGATCAATCACGTAAAATCTATGAAGCATTAAAGAAAAAAGGTCTGCCTGTTGCTCTTGTCGAGTACGAAGGAGAACAACACGGTTTTC
upper sequence: GLYMA18G11480.1 (Glycine max), 3'ss of exon 16
lower sequence: Vv18s0001g11140.t01 (Vitis vinifera), 3'ss of exon 16
gttagtaaca-atgctattat----tattttcccttaccatattgtctactt-attcccaaatctatatataatcttcaaaaatcatcttgacaaatatattctgtgcattgcagGTTGTGCCACCGGATCAAGCTCGGAAAATATACCAGGCGGTGAAAGAAAAAGGTGTGCCAGTTGCTCTTGTTGAGTATGAAGGAGAACAACACGGTTTCC
||||| || || | || | || |||| | | || | | | | | | | ||| |||||| ||| ||||| |||||||||| || || | ||||||||| ||||| |||||||| |||| ||||| ||| |||| ||||||||||| |||||||||||||||||||| || || |
-ccagtaatggattgcataaagaagtagtgggttccacaatatcgcccttttcagcattgattttgttcctgaatttctaaaatctc--------ataaattct------tgcagGTTGTACCTCCAGTTCAAGCTCGTAAAATCTACCAGGCATTGAAGGAAAAGGGTTTGCCTGTTGCTCTTGTGGAGTATGAAGGAGAACAACATGGATTTC
upper sequence: GLYMA18G11480.1 (Glycine max), 3'ss of exon 16
lower sequence: Vv18s0001g11150.t01 (Vitis vinifera), 3'ss of exon 16
gttagtaacaatgctattattattttcccttaccatattgtctact-tattcccaaatctatatataatcttcaaaaatcatcttgacaaatatattctgtgcattgcagGTTGTGCCACCGGATCAAGCTCGGAAAATATACCAGGCGGTGAAAGAAAAAGGTGTGCCAGTTGCTCTTGTTGAGTATGAAGGAGAACAACACGGTTTCC
| ||||| | |||| | | | || ||| |||||| || | | || || | | ||| |||| | | | | |||||| || || || || |||||||| ||||| |||| ||| |||| |||||||| |||| ||||||||||| ||||||||||||||||||| ||||| |
--catctgcaatgg----actattgactaaagcagcaggttccactacattccc--atttttcagcaacatttagttccaaatttg--aaatttctcgtcttttccgcagGTGGTACCCCCAGAGCAAGCTCGTAAAATCTACCTGGCACTGAAGAAAAAAGGTTTGCCTGTTGCTCTTGTGCAGTATGAAGGAGAACAACATGGTTTTC atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.aatctatatataatcttcaaaaatcatcttgacaaatatattctgtgcattgcagGTTGTGCCACCGGATCAAGCTCGGAAAATATACCAGGCGGTGAAAGAAAAAGGTGTGCCAGTTGCTCTTGTTGAGTATGAAGGAGAACAACACGGTTTCC
tcttgac putative branch site (score: 3)
atatataatcttcaaa 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gttagtaacaatgctattattattttcccttaccatattgtctacttattcccaaatctatatataatcttcaaaaatcatcttgacaaatatattctgtgcattgcagGTTGTGCCACCGGATCAAGCTCGGAAAATATACCAGGCGGTGAAAGAAAAAGGTGTGCCAGTTGCTCTTGTTGAGTATGAAGGAGAACAACACGGTTTCC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAA