Sequence
atgc intronic sequence ATGC exonic sequencegtgagataaattacaatatttctcaggagtggtgcacttcatttttggctttactaactatgcagtctctccccacctgtgggcctaattatagGTTTTGAAAGTGAAAGAAGAAAGTTTAGTACCAGCAAATCCTGATATCCTTGATGGGGTGGATGACCTCATGCAACTTAGTTATTTAAATGAACCGTCAG
Basic information
species | Glycine max |
transcript | GLYMA09G42180.1 |
intron # | 1 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA09G42180.1 (Glycine max), 3'ss of exon 1
lower sequence: GRMZM2G139583_T02 (Zea mays), 3'ss of exon 2
gtgagataaattacaatatttctcaggagtggtgcacttcatttttggctttactaactatgcagtc-tctccccacctgtgggcctaattatagGTTTTGAAAGTGAAAGAAGAAAGTTTAGTACCAGCAAATCCTGATATCCTTGATGGGGTGGATGACCTCATGCAACTTAGTTATTTAAATGAACCGTCAG
||| || || |||||| || | || || | | ||| ||| | | || || | || || |||| ||| | ||||| ||| || | ||| ||||||||||| || |||||||| ||||||||||| ||||| || |||||| ||| |||||| ||||
-----gtaagttgcag-atttcttttaagag-------tctgttctataatcactggaagcatggtcatttgaccgccctt---ccctttttaagGTACTGAGATTGAAAACAGAGAGCCTTCAACCTGCAAATCCTGAAATTCTTGATGGAGTGGATGACCTTATGCAGCTAAGTTATCTAAGTGAACCATCAG
upper sequence: GLYMA09G42180.1 (Glycine max), 3'ss of exon 1
lower sequence: GRMZM2G113202_T01 (Zea mays), 3'ss of exon 2
gtgagataaattaca-atatttctcaggagtggtgcacttcatttttggctttactaactatgcagtctctccccacctgtgggcctaattatagGTTTTGAAAGTGAAAGAAGAAAGTTTAGTACCAGCAAATCCTGATATCCTTGATGGGGTGGATGACCTCATGCAACTTAGTTATTTAAATGAACCGTCAG
||| || || || | | || | || | || | || | | || || | ||||||| | || || |||| ||| | ||||| || || || ||| ||||||||||| || |||||||| |||||||| || ||||| || |||||| ||| |||||| ||||
-----gtaagttgcagatttctttctaagatagtctgttctataatca-ctggaagcatgat-catttgacccccaccctt---ccctttttaagGTACTGAGATTGAAAACCGAGTGTCTACAACCTGCAAATCCTGAAATTCTTGATGGAGTGGATGATCTTATGCAGCTAAGTTATCTAAGTGAACCATCAG
upper sequence: GLYMA09G42180.1 (Glycine max), 3'ss of exon 1
lower sequence: AT3G19960.2 (Arabidopsis thaliana), 3'ss of exon 3
gtgagataaattacaatatttctcaggagtggtgcacttcatttttggctttactaactatgcagtctctccccacctgtgggcctaattatagGTTTTGAAAGTGAAAGAAGAAAGTTTAGTACCAGCAAATCCTGATATCCTTGATGGGGTGGATGACCTCATGCAACTTAGTTATTTAAATGAACCGTCAG
|| || ||| || ||||||| ||| | | || ||||||| || ||| ||| | || | | | | | ||||| | ||||| | | ||| | | ||||||| |||||||||||||| |||||||| ||||| || || ||||| |||||||| |||||||| || ||||
gtaag-taactttttgtatttctaagg--tagccaggttaatttttg--------aagtatttgatctgaaactactttcaaacttgaa-acagGTTATAAAAGTCATATCAGAGACTCTAGTACCTGCAAATCCTGATATTCTTGATGGAGTGGACGATCTTATGCAGCTTAGTTACTTAAATGAGCCATCAG
upper sequence: GLYMA09G42180.1 (Glycine max), 3'ss of exon 1
lower sequence: AT1G50360.1 (Arabidopsis thaliana), 3'ss of exon 3
gtgagataaattacaatatttctcaggagtggtgcacttcatttttggctttactaactatgcagtctctccccacctgtgggcctaatt--atagGTTTTGAAAGTGAAAGAAGAAAGTTTAGTACCAGCAAATCCTGATATCCTTGATGGGGTGGATGACCTCATGCAACTTAGTTATTTAAATGAACCGTCAG
|| || | || | ||| | || | || | ||| ||| ||| | | || | | || | | | ||| | ||||||| ||||| ||| ||| | ||||||||| |||||||||||||| |||||||| || || || ||||||||||| |||||||||||||| || |||
gtaagtgattttgttaaattccctgggtg-aatgtaaactattattg-------taagtgtttgatcggaaactatctcttcacttgattcaacagGTTTTAAAAGTCAAATCAGAGACTTTAGTACCTGCAAATCCTGATATTCTTGATGGAGTAGACGATCTCATGCAACTAAGTTATTTAAATGAGCCAGCAG
upper sequence: GLYMA09G42180.1 (Glycine max), 3'ss of exon 1
lower sequence: Vv10s0071g00210.t01 (Vitis vinifera), 3'ss of exon 2
gtgagataaattacaatatttctcaggagtggt-gcacttcatttttggctttactaactatgcagtctctccccacctgtgggcctaattatagGTTTTGAAAGTGAAAGAAGAAAGTTTAGTACCAGCAAATCCTGATATCCTTGATGGGGTGGATGACCTCATGCAACTTAGTTATTTAAATGAACCGTCAG
|| || || | | | | | || || | | | ||| || | | | || | | ||| || |||| |||||||| || ||||| || || | |||| ||||| || ||||| ||||| || || |||||||| |||||||||||||| |||||||| || || |
gtaagtaaactaatgcaaacttggatgattgattgtatgtcaa---tgaatctgttgtttacctttttattttgcactggtt--ttcaattttagGTTTTAAAGGTGAATACTGACAGCCTGTTACCTGCAAACCCCGATATACTTGACGGTGTAGATGACCTTATGCAACTTAGTTACTTAAATGAGCCATCGG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.catttttggctttactaactatgcagtctctccccacctgtgggcctaattatagGTTTTGAAAGTGAAAGAAGAAAGTTTAGTACCAGCAAATCCTGATATCCTTGATGGGGTGGATGACCTCATGCAACTTAGTTATTTAAATGAACCGTCAG
taattata 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtgagataaattacaatatttctcaggagtggtgcacttcatttttggctttactaactatgcagtctctccccacctgtgggcctaattatagGTTTTGAAAGTGAAAGAAGAAAGTTTAGTACCAGCAAATCCTGATATCCTTGATGGGGTGGATGACCTCATGCAACTTAGTTATTTAAATGAACCGTCAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGTGGA