Sequence
atgc intronic sequence ATGC exonic sequence...ttttaagttaaatgaactattgtttttgttagtcttcagagagagaattattttctatcttggttatggttaaaagttggaaatgaactttttattgcagATAAGGGTCATTGATCGAAACTGTGAAATTCCTCATGAGGGTCCTTTCTGTGATCTTATGTGGAGTGATCCTGAAGATATTGAAACATGGGCAGTCAGTC
Basic information
species | Glycine max |
transcript | GLYMA10G43480.1 |
intron # | 6 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA10G43480.1 (Glycine max), 3'ss of exon 6
lower sequence: LOC_Os01g49690.1 (Oryza sativa), 3'ss of exon 6
--ttttaagttaaatgaactattgtttttgttagtcttcagagagagaattattttctatcttggt-tatggttaaaagttggaaatgaactttttattgcagATAAGGGTCATTGATCGAAACTGTGAAATTCCTCATGAGGGTCCTTTCTGTGATCTTATGTGGAGTGATCCTGAAGATATTGAAACATGGGCAGTCAGTC
| || | | | || |||| | | |||| | | | | || || || | | | | || ||||| || |||||||| || ||||||||||||||||| ||||||||||||||||| ||||||||||| |||||||| || || |||||||| || || |
agatatattgttgtcagataagaattaaaaaccgtctc--aacgcaatattacaatgaaattaatcatgtgattgaatatccttgttaattctattgac-cagATTCGGACGATTGATCGCAATTGTGAAATTCCTCATGAAGGTCCTTTCTGTGATCTAATGTGGAGTGACCCTGAAGAAATAGAGACATGGGCTGTTAGCC
upper sequence: GLYMA10G43480.1 (Glycine max), 3'ss of exon 6
lower sequence: GRMZM2G055905_T04 (Zea mays), 3'ss of exon 7
-----------ttttaagtta------aatgaactattgtttttgttagtcttcagagagagaattattttctatcttggttatggttaaa----agttggaaatgaactttttattgcagATAAGGGTCATTGATCGAAACTGTGAAATTCCTCATGAGGGTCCTTTCTGTGATCTTATGTGGAGTGATCCTGAAGATATTGAAACATGGGCAGTCAGTC
|| | | | | | |||| | | | | | | || || || ||||||| | | ||| | | | || | | | ||||| | |||||| | |||||||| || ||||||||||| ||||| ||||||||||| || |||||||||||||| ||||| || || || |||||||| || ||||
gttcgtagcatttctgactcatttcttgaagaacagtagagtgcatgattatttggat-gattcttattttgactaattgtttcaatgagattgaagctttgattatcttttttttaccagATACGAACAATTGATCGCAATTGTGAAATTCCCCATGAAGGTCCTTTCTGCGACCTTATGTGGAGTGACCCTGAGGAGATAGAGACATGGGCTGTTAGTC
upper sequence: GLYMA10G43480.1 (Glycine max), 3'ss of exon 6
lower sequence: GRMZM2G518717_T03 (Zea mays), 3'ss of exon 2
ttttaagttaaatgaactattgtttttgttagtcttcagagagagaattattttctatcttggttatggttaaaagttggaaatgaactttttattgc-agATAAGGGTCATTGATCGAAACTGTGAAATTCCTCATGAGGGTCCTTTCTGTGATCTTATGTGGAGTGATCCTGAAGATATTGAAACATGGGCAGTCAGTC
| | | | || || | | | | | || || ||||||| | ||| | | | | ||| | || | | ||||| | |||||||| || ||||||||||| ||||| || |||||||| ||||||||||||||||| ||||| || || || |||||||| || ||||
actcatttcgtgaagaatagtgagtgcatgattatgtggat-gattcttattttgacttaatgtttcaatgagattgaagctttgattatcttttcaccagATACGAACGATTGATCGCAATTGTGAAATTCCCCATGAAGGCCCTTTCTGCGATCTTATGTGGAGTGACCCTGAGGAGATAGAGACATGGGCTGTTAGTC
upper sequence: GLYMA10G43480.1 (Glycine max), 3'ss of exon 6
lower sequence: GRMZM2G055905_T02 (Zea mays), 3'ss of exon 6
ttttaagttaaatgaactattgtttttgttagtcttcagagagagaattattttctatcttggttatggttaaa----agttggaaatgaactttttattgcagATAAGGGTCATTGATCGAAACTGTGAAATTCCTCATGAGGGTCCTTTCTGTGATCTTATGTGGAGTGATCCTGAAGATATTGAAACATGGGCAGTCAGTC
| || || |||| | | | | | | || || || ||||||| | | ||| | | | || | | | ||||| | |||||| | |||||||| || ||||||||||| ||||| ||||||||||| || |||||||||||||| ||||| || || || |||||||| || ||||
--atttcttgaa-gaacagtagagtgcatgattatttggat-gattcttattttgactaattgtttcaatgagattgaagctttgattatcttttttttaccagATACGAACAATTGATCGCAATTGTGAAATTCCCCATGAAGGTCCTTTCTGCGACCTTATGTGGAGTGACCCTGAGGAGATAGAGACATGGGCTGTTAGTC
upper sequence: GLYMA10G43480.1 (Glycine max), 3'ss of exon 6
lower sequence: AT3G19980.1 (Arabidopsis thaliana), 3'ss of exon 6
ttttaagttaaa-tgaactattgtttttgttagtcttcagagagagaattat-tttctatcttggt-tatggttaaaagttggaa-----atgaactttttattg----cagATAAGGGTCATTGATCGAAACTGTGAAATTCCTCATGAGGGTCCTTTCTGTGATCTTATGTGGAGTGATCCTGAAGATATTGAAACATGGGCAGTCAGTC
|||||| | || || || | | | |||| | |||||| ||||| ||||| | | |||| | || | || | | | ||||||| | || || ||||| || |||||||||||||| || || || || ||||||||||||||||||||||||||||||||||||||||| || ||||
------gttaaactctgcttttattgcttgtggctttcaccc-gtcaattatgcttctagcttggcatgttattaaggtcctccactcacatagatttgctgtgggctctagATAAGACTGATCGAGCGAAATTGCGAAATTCCTCATGAAGGGCCCTTTTGCGATCTTATGTGGAGTGATCCTGAAGATATTGAAACATGGGCGGTTAGTC
upper sequence: GLYMA10G43480.1 (Glycine max), 3'ss of exon 6
lower sequence: AT1G50370.1 (Arabidopsis thaliana), 3'ss of exon 6
ttttaagttaaatgaactattgtttttgttagtcttca--gagagagaattattttctatc---ttggttatggttaaaagttggaaatga-actttttattgcagATAAGGGTCATTGATCGAAACTGTGAAATTCCTCATGAGGGTCCTTTCTGTGATCTTATGTGGAGTGATCCTGAAGATATTGAAACATGGGCAGTCAGTC
|||| | | | || | || || |||| | || |||||| || || | | || | | | ||| | ||| | | ||||||| | ||||| || || || ||||| || ||||| || || ||||||||||||||||||||||||||||||||||||||||||||||| |||||||
-gttaaaatgtgctattttaaattacttttggttttcaccatgcaagtgttatttatgattagattaaatctcatttactcatttagatgttattttgttctctagATAAGATTGATTGAGCGGAATTGCGAAATACCGCATGAAGGACCCTTCTGTGATCTTATGTGGAGTGATCCTGAAGATATTGAAACATGGGCTGTCAGTC
upper sequence: GLYMA10G43480.1 (Glycine max), 3'ss of exon 6
lower sequence: Vv10s0071g00950.t01 (Vitis vinifera), 3'ss of exon 6
-ttttaagttaaatgaactattgtttttgttagtcttcagagagagaattattttctatcttggttatggttaaaagttggaaatgaacttt-ttattgcagATAAGGGTCATTGATCGAAACTGTGAAATTCCTCATGAGGGTCCTTTCTGTGATCTTATGTGGAGTGATCCTGAAGATATTGAAACATGGGCAGTCAGTC
| |||| | | | ||| | || | ||| | |||| | | | | || ||| || | || |||||||| ||||||||||| ||||| |||||||||||||||||||| || |||||||||||||||||||||||||||||||| ||||| || |||||||||||||
tgtctaagc--agttgttttctgtgcccaagaatccaccatgagcaagatattaacctaagttttggcatcttaattttgtttctgcctctcatttttgcagATTAGGGTCATTGAACGAAATTGTGAAATTCCTCATGAGGGGCCATTCTGTGATCTTATGTGGAGTGATCCTGAAGACATTGAGACGTGGGCAGTCAGTC
upper sequence: GLYMA10G43480.1 (Glycine max), 3'ss of exon 6
lower sequence: PP1S207_36V6.1 (Physcomitrella patens), 3'ss of exon 6
ttttaagttaaatgaactattgtttttgttagtcttcagagagagaattattttctatcttggttatggttaaaagttggaaatg--aactttttat------tgcagATAAGGGTCATTGATCGAAACTGTGAAATTCCTCATGAGGGTCCTTTCTGTGATCTTATGTGGAGTGATCCTGAAGATATTGAAACATGGGCAGTCAGTC
| |||| || | | || | |||| | | || ||| ||| |||||| | || | || | | || | || ||||||| ||||| || || | | ||||| ||||||||||| || || |||||||| | ||||||||||||||||| ||||| ||||| ||||| || || |
------ctacaatgtgctg--agtctagtcaatcttttaattcgtggattttgtcttgcttcattatggatgaatttgaaaagtttcactttctcataatgtgtgcagATTAGGGTGATAGAGAGGCAGTGTGAGATTCCTCATGAAGGGCCATTCTGTGACTTGATGTGGAGTGATCCTGAGGATATCGAAACTTGGGCTGTTAGCC
upper sequence: GLYMA10G43480.1 (Glycine max), 3'ss of exon 6
lower sequence: PP1S31_220V6.1 (Physcomitrella patens), 3'ss of exon 6
ttttaagttaaatgaactattgtttttgttagtcttcagagagagaattattttctatcttggttatggttaaaagttg---gaaatga------actttttattgcagATAAGGGTCATTGATCGAAACTGTGAAATTCCTCATGAGGGTCCTTTCTGTGATCTTATGTGGAGTGATCCTGAAGATATTGAAACATGGGCAGTCAGTC
| ||| | ||| | ||| | ||| ||| | | || || | || ||| ||| | || | |||| || | | |||| |||||||| ||||| ||||| | | ||||| |||||||| ||||| || || |||||||| ||||||||||| ||||| ||||| || || ||||| || ||||
tgttatcctgaata---tcttgatcctgt-agttt-----gtgaattttttgtttcatcatggatgcaattgatagttactcaaagccatttgttatctttttttgcagATTAGGGTGATTGAGAGGCAGTGTGAGATTCCTCACGAGGGGCCATTTTGTGATCTGATGTGGAGTGACCCTGAGGATATCGAGACTTGGGCTGTTAGTC atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.aattattttctatcttggttatggttaaaagttggaaatgaactttttattgcagATAAGGGTCATTGATCGAAACTGTGAAATTCCTCATGAGGGTCCTTTCTGTGATCTTATGTGGAGTGATCCTGAAGATATTGAAACATGGGCAGTCAGTC
ctttttatt CT-rich tract
aaatgaactttttatt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
ttttaagttaaatgaactattgtttttgttagtcttcagagagagaattattttctatcttggttatggttaaaagttggaaatgaactttttattgcagATAAGGGTCATTGATCGAAACTGTGAAATTCCTCATGAGGGTCCTTTCTGTGATCTTATGTGGAGTGATCCTGAAGATATTGAAACATGGGCAGTCAGTC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGA
- - - - - aatgaac
- - - - - - - - - - - - - - - -gtcttca
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ggttatg