Sequence
atgc intronic sequence ATGC exonic sequencegttttactcaggaacccatcacctttctgtgcttgttacaaagtatttcataatattgatcattttaaaactacagGGGATGGGGTTTTTAGCGGGACTTTTGCTTCTTTATATGAGCGAGGAGGATGCATTTTGGTTGTTGGTGGCATTGCTAAAAGGAGCCGTTCATGCTCCAA
Basic information
species | Glycine max |
transcript | GLYMA13G07090.1 |
intron # | 3 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA13G07090.1 (Glycine max), 3'ss of exon 3
lower sequence: LOC_Os08g31840.2 (Oryza sativa), 3'ss of exon 4
gttttactcagga--acccatcacctttctgtgcttgttacaaagtatttcataatat-tgatcattttaaaac--------tacagGGGATGGGGTTTTTAGCGGGACTTTTGCTTCTTTATATGAGCGAGGAGGATGCATTTTGGTTGTTGGTGGCATTGCTAAAAGGAGCCGTTCATGCTCCAA
|||| | | | | | | ||| | | | | || |||||| || || ||| | | ||||| ||||| |||||||| || | | |||||||||||||| || || |||||||||||||| || || || ||||| || ||||| |||||||| ||||
gtttgtgttaaaactgctgactagttttaggatataaacttattctgttgagtaatatgtgttctcttttgcataatcatgatgcagGGAATGGGATTTTTAGCTGGCTTGCTACTTCTTTATATGAGTGAAGAAGATGCATTTTGGTTATTAGTTGCTTTGCTGAAGGGAGCTGTTCATGCGCCAA
upper sequence: GLYMA13G07090.1 (Glycine max), 3'ss of exon 3
lower sequence: GRMZM2G047223_T02 (Zea mays), 3'ss of exon 4
gttttactcaggaacccatcacctttctgtgcttgttacaaagtatttc----ataatattg-atcattttaaaa-------ctacagGGGATGGGGTTTTTAGCGGGACTTTTGCTTCTTTATATGAGCGAGGAGGATGCATTTTGGTTGTTGGTGGCATTGCTAAAAGGAGCCGTTCATGCTCCAA
||| | | | | |||| | | | | | || | | || |||||||| || ||| | | | ||||| ||||| |||||||| || || |||||||||||||||| |||||||||||||| ||||| || || || |||||||| ||||| || ||||| ||||
-gtttgttttgagttcggtgacctattttttcagatagaaagatctctctggaataatattctattgtttacacaattcattttgcagGGAATGGGATTTTTAGCTGGGCTGCTGCTTCTTTATATGAGTGAGGAGGATGCATTCTGGTTATTAGTCGCGTTGCTAAAGGGAGCTGTCCATGCACCAA
upper sequence: GLYMA13G07090.1 (Glycine max), 3'ss of exon 3
lower sequence: AT3G02460.1 (Arabidopsis thaliana), 3'ss of exon 4
--gttttactcaggaacccatcacctttc---tgtgcttgttacaaagtatttca-taatattgatcattttaaaa-ctacagGGGATGGGGTTTTTAGCGGGACTTTTGCTTCTTTATATGAGCGAGGAGGATGCATTTTGGTTGTTGGTGGCATTGCTAAAAGGAGCCGTTCATGCTCCAA
| | || | | |||| | | | | ||||| | ||| ||| || ||| ||| | || ||||||||||||||| |||| || | |||||||| ||||||||||| || ||||| || ||||| || || ||||| || |||||||| |||||||||||||
gtctatcctctagatatttcccttgtttcccatttttctttcttttagtatgggactaagattcatgattctaatatctgcagGGGATGGGGTTTATAGCCGGTTTGTTGCTTCTCTATATGAGCGAAGAAGATGCCTTCTGGTTATTAGTTGCATTACTTAAAGGAGCTGTTCATGCTCCAA
upper sequence: GLYMA13G07090.1 (Glycine max), 3'ss of exon 3
lower sequence: AT5G15930.1 (Arabidopsis thaliana), 3'ss of exon 4
gttttactcaggaacccatcacctttctgtgcttgttacaaa--gta----tttcataatattgatcattttaaaacta---cagGGGATGGGGTTTTTAGCGGGACTTTTGCTTCTTTATATGAGCGAGGAGGATGCATTTTGGTTGTTGGTGGCATTGCTAAAAGGAGCCGTTCATGCTCCAA
|| || | || | || | | | ||| | | ||| || | || | | || | ||||| || ||||| ||||| || |||| || | |||||||||||||||||||| || |||||||| ||||| || || ||||| || |||||||| || || | ||||
gtatttccagagatcttttcctttattcttatttgcccaagatggtactaattacgaaagactcatggtactaaaaataatgcagGGAATGGGTTTCATAGCCGGTTTGTTGCTTCTTTATATGAGCGAAGAAGATGCATTCTGGTTATTAGTTGCATTACTCAAAGGAGCTGTCCACTCCCCAA
upper sequence: GLYMA13G07090.1 (Glycine max), 3'ss of exon 3
lower sequence: Vv14s0083g00540.t01 (Vitis vinifera), 3'ss of exon 4
gtttta--ctcaggaacc-catcacctttctgt--gcttgttacaaagtatttcataatattg-atcatt----ttaaaactacagGGGATGGGGTTTTTAGCGGGACTTTTGCTTCTTTATATGAGCGAGGAGGATGCATTTTGGTTGTTGGTGGCATTGCTAAAAGGAGCCGTTCATGCTCCAA
|||| |||| | | | |||||| |||| | || || | || | || | |||| || | || || | ||||| ||||| |||||||| || | |||||||||||||||| || || |||||||| |||||| |||| ||||| || |||||||| |||||||||||||
gtttggatctcatgtatctcatcactcttctatttactgtttgtaggatactgaatgacattggattggtatcgtttgaaatgcagGGAATGGGATTTTTAGCTGGCTTACTGCTTCTTTATATGAGTGAAGAAGATGCATTCTGGTTGATGGTTGCATTACTTAAAGGAGCTGTTCATGCTCCAA atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.cctttctgtgcttgttacaaagtatttcataatattgatcattttaaaactacagGGGATGGGGTTTTTAGCGGGACTTTTGCTTCTTTATATGAGCGAGGAGGATGCATTTTGGTTGTTGGTGGCATTGCTAAAAGGAGCCGTTCATGCTCCAA
tattgat putative branch site (score: 3)
ttacaaagtatttcat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gttttactcaggaacccatcacctttctgtgcttgttacaaagtatttcataatattgatcattttaaaactacagGGGATGGGGTTTTTAGCGGGACTTTTGCTTCTTTATATGAGCGAGGAGGATGCATTTTGGTTGTTGGTGGCATTGCTAAAAGGAGCCGTTCATGCTCCAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGTGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAG