Sequence
atgc intronic sequence ATGC exonic sequence...gtgtgtaatagcctcatttaaaatggtttcgtttttatgattgctttgttgttgttttgtgtattgtagccattaacgtgcctccttgttgacattacagGTGGTAGAACGTTTCCATGAACTGTTTGCCCAAACCAAGTATAAAGAAGCAGCTGAGCTTGCTGCTGAGTCTCCACAAGGAATCCTTCGCACACCTGATA
Basic information
species | Glycine max |
transcript | GLYMA11G35460.1 |
intron # | 10 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA11G35460.1 (Glycine max), 3'ss of exon 10
lower sequence: GRMZM2G057576_T02 (Zea mays), 3'ss of exon 8
gtgtgtaatagcctcatttaaaatggtttcgtttttatgattgctttgttgttgttttgtgtattgtagccattaacgt-gcctccttgttgacattacagGTGGTAGAACGTTTCCATGAACTGTTTGCCCAAACCAAGTATAAAGAAGCAGCTGAGCTTGCTGCTGAGTCTCCACAAGGAATCCTTCGCACACCTGATA
| || | ||| ||| | | | | | | | | | | ||||| | | | | | | | | | | ||||| || || | ||||| ||||||||||| ||||| || || || |||||||||||||| ||||| |||||||| || || || | | || ||||| |
-ctaatgatgctttattttgtggaagttgcatactatgagtagttagacttctatggttaatattgaatagagtttcatcaaattatgaattgtactgcagGTTGTGCAAAGGTTCCAGGAACTGTTTGCGCAAACAAAATACAAGGAAGCAGCTGAGCTGGCTGCAGAGTCTCCGCAGGGCCTCTTGAGGACTCCTGAAA
upper sequence: GLYMA11G35460.1 (Glycine max), 3'ss of exon 10
lower sequence: AT3G08530.1 (Arabidopsis thaliana), 3'ss of exon 10
----------------gtgtgta-atagcctcatttaa--aatggtttcgttttta--tgattgctttgt---------tgttgttttgtgtattgtagccattaacgtgcctccttgttgacattacagGTGGTAGAACGTTTCCATGAACTGTTTGCCCAAACCAAGTATAAAGAAGCAGCTGAGCTTGCTGCTGAGTCTCCACAAGGAATCCTTCGCACACCTGATA
|| | | | ||| | || ||| | | ||| ||| || |||| ||| ||| || | || || | | | || || | || || |||| || | || ||||| || |||| || ||||| ||||| || || || ||||||||||||||||| ||||| |||||||| || | ||||||||||
gtatgcgatgtttatcatggatctgttgtctcggtgaagtaattatatagttgttaaatggcagcttgaagaaaaaaaatgtcatttggtattgtgaagtttctcatat-tctgctcg--gatgttgtagGTTGTCCAGCGGTTCCAGGAGTTGTTCGCTCAAACAAAGTACAAGGAGGCTGCTGAGCTTGCTGCTGAATCTCCTCAAGGAATTCTAAGGACACCTGATA
upper sequence: GLYMA11G35460.1 (Glycine max), 3'ss of exon 10
lower sequence: Vv13s0067g01290.t01 (Vitis vinifera), 3'ss of exon 10
------gtgtgtaatagcctcatttaaaatggtttcgtttttatgattgctttgttgttgttttgtgtattgtagccattaacgtgcctccttgttgacattacagGTGGTAGAACGTTTCCATGAACTGTTTGCCCAAACCAAGTATAAAGAAGCAGCTGAGCTTGCTGCTGAGTCTCCACAAGGAATCCTTCGCACACCTGATA
||| | ||| |||| | || | ||| || | ||| || || | | | | | | || | |||| | || ||||| || | |||||||| ||| ||||||| || || |||||||| || || ||||||||||||||||| |||||||||||||| || || ||||| || |
agaatcatgtttcatatagtcatggtggaaatttatactgtta-aatcattatgtagtctttgcatatttggaatctgatagcctgccatttc-----tatatcagGTTGTCCAGCGTTTCCAAGAATTGTTTGCTCAGACAAAGTATAAGGAGGCTGCTGAGCTTGCTGCTGAATCTCCACAAGGAATTCTCCGTACACCGGACA
upper sequence: GLYMA11G35460.1 (Glycine max), 3'ss of exon 10
lower sequence: EFJ24508 (Selaginella moellendorffii), 3'ss of exon 10
gtgtgtaatagcctcatttaaaatggtttcgtttttatgattgctttgttgttgttttgtgtattgtagccattaacgtgcctccttgttgacattacagGTGGTAGAACGTTTCCATGAACTGTTTGCCCAAACCAAGTATAAAGAAGCAGCTGAGCTTGCTGCTGAGTCTCCACAAGGAATCCTTCGCACACCTGATA
|| || |||||| ||| | || | ||| | | | || | ||| || | | | | |||| || |||| || || || | || |||| ||||| |||||||| || |||||||| |||||||| || ||||||||||||||||| | ||| |
-------------------------gtaacgcttttat-----cttcgatgat-ctttctctttgctacctcttactgtatcgttctatgtgagt---agGTTGTGCAACGGTTTCAGGAGTTATTCCAACAAATGAAGTACAAAGAAGCTGCGGAGCTTGCAGCTGAGTCCCCTCAAGGAATCCTTCGCACGCATGACA
upper sequence: GLYMA11G35460.1 (Glycine max), 3'ss of exon 10
lower sequence: EFJ13237 (Selaginella moellendorffii), 3'ss of exon 10
gtgtgtaatagcctcatttaaaatggtttcgtttttatgattgctttgttgttgttttgtgtattgtagccattaacgtgcctccttgttgacattacagGTGGTAGAACGTTTCCATGAACTGTTTGCCCAAACCAAGTATAAAGAAGCAGCTGAGCTTGCTGCTGAGTCTCCACAAGGAATCCTTCGCACACCTGATA
|| | |||||| ||| | || | ||| | | | || | ||| || | | | | |||| || |||| || || || | || |||| ||||| |||||||| || |||||||| |||||||| || ||||||||||||||||| | ||| |
-------------------------gtaacccttttat-----cttcgatgat-ctttctctttgctacctcttactgtatcgttctatgtgagt---agGTTGTGCAACGGTTTCAGGAGTTATTCCAACAAATGAAGTACAAAGAAGCTGCGGAGCTTGCAGCTGAGTCCCCTCAAGGAATCCTTCGCACGCATGACA atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ttgttgttgttttgtgtattgtagccattaacgtgcctccttgttgacattacagGTGGTAGAACGTTTCCATGAACTGTTTGCCCAAACCAAGTATAAAGAAGCAGCTGAGCTTGCTGCTGAGTCTCCACAAGGAATCCTTCGCACACCTGATA
ttgtttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtgtgtaatagcctcatttaaaatggtttcgtttttatgattgctttgttgttgttttgtgtattgtagccattaacgtgcctccttgttgacattacagGTGGTAGAACGTTTCCATGAACTGTTTGCCCAAACCAAGTATAAAGAAGCAGCTGAGCTTGCTGCTGAGTCTCCACAAGGAATCCTTCGCACACCTGATA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGCTT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAA
gtgtgta
- - - - - - - - - - - - - - - - - - -tgattgc
- - - - - - - - - - - - - - - - - - - - - - - -gttgttg
- - - - - - - - - - - - - - - - - - - - - - - - - - - ttttgtg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -agccatt