Sequence
atgc intronic sequence ATGC exonic sequence...gtgtgtaatagcctcatttaaaatggtttagtttttttattgctttgtttttttttgtgtgtattttactcattaacatgcctccttgttgacattacagGTGGTAGAACGTTTCCATGAACTGTTTGCCCAAACAAAGTATAAAGAAGCAGCTGAACTTGCTGCTGAGTCTCCGCAAGGAATCCTTCGCACACCTGATA
Basic information
species | Glycine max |
transcript | GLYMA18G02960.1 |
intron # | 10 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA18G02960.1 (Glycine max), 3'ss of exon 10
lower sequence: GRMZM2G057576_T02 (Zea mays), 3'ss of exon 8
gtgtgtaatagcctcatttaaaatggtttagtttttttattgctttgtttttttttgtgtgtattttactcattaacat-gcctccttgttgacattacagGTGGTAGAACGTTTCCATGAACTGTTTGCCCAAACAAAGTATAAAGAAGCAGCTGAACTTGCTGCTGAGTCTCCGCAAGGAATCCTTCGCACACCTGATA
| || | ||| ||| | | | | | || | || | | || |||| | | | ||| | | | | | ||||| || || | ||||| ||||||||||| |||||||| || || ||||||||||| || ||||| ||||||||||| || || | | || ||||| |
-ctaatgatgctttattttgtggaagttgcatactatgagtagttagacttctatggttaatattgaatagagtttcatcaaattatgaattgtactgcagGTTGTGCAAAGGTTCCAGGAACTGTTTGCGCAAACAAAATACAAGGAAGCAGCTGAGCTGGCTGCAGAGTCTCCGCAGGGCCTCTTGAGGACTCCTGAAA
upper sequence: GLYMA18G02960.1 (Glycine max), 3'ss of exon 10
lower sequence: AT3G08530.1 (Arabidopsis thaliana), 3'ss of exon 10
---------gtgtgtaatagcctcatt--taaaatggtttagtttttttattgctttgtttttttttgtgtgta-----ttttactcattaacatg----cctccttgtt-------gacattacagGTGGTAGAACGTTTCCATGAACTGTTTGCCCAAACAAAGTATAAAGAAGCAGCTGAACTTGCTGCTGAGTCTCCGCAAGGAATCCTTCGCACACCTGATA
|| | | || | || || || || | | ||| | | ||| | | | | | || || | | || || || |||| || | || ||||| || |||| || ||||||||||| || || || ||||| ||||||||||| ||||| |||||||| || | ||||||||||
gtatgcgatgtttatcatggatctgttgtctcggtgaagtaattatatagttgttaaatggcagcttgaagaaaaaaaatgtcatttggtattgtgaagtttctcatattctgctcggatgttgtagGTTGTCCAGCGGTTCCAGGAGTTGTTCGCTCAAACAAAGTACAAGGAGGCTGCTGAGCTTGCTGCTGAATCTCCTCAAGGAATTCTAAGGACACCTGATA
upper sequence: GLYMA18G02960.1 (Glycine max), 3'ss of exon 10
lower sequence: Vv13s0067g01290.t01 (Vitis vinifera), 3'ss of exon 10
------gtgtgtaatagcctcatttaaaatggtttagtttttttattgctttgtttttttttgtgtgtattttactcattaacatgcctccttgttgacattacagGTGGTAGAACGTTTCCATGAACTGTTTGCCCAAACAAAGTATAAAGAAGCAGCTGAACTTGCTGCTGAGTCTCCGCAAGGAATCCTTCGCACACCTGATA
||| | ||| |||| | || | || || | ||| | ||| | | | | | || | |||| | || ||||| || | |||||||| ||| ||||||| || ||||||||||| || || ||||| ||||||||||| ||||| |||||||| || || ||||| || |
agaatcatgtttcatatagtcatggtggaaatttatactgttaaatcattatgtagtcttt-gcatatttggaatctgatagcctgccatttc-----tatatcagGTTGTCCAGCGTTTCCAAGAATTGTTTGCTCAGACAAAGTATAAGGAGGCTGCTGAGCTTGCTGCTGAATCTCCACAAGGAATTCTCCGTACACCGGACA
upper sequence: GLYMA18G02960.1 (Glycine max), 3'ss of exon 10
lower sequence: EFJ24508 (Selaginella moellendorffii), 3'ss of exon 10
gtgtgtaatagcctcatttaaaatggtttagtttttttattgctttgtttttttttgtgtgtattttactcattaacatgcctccttgttgacattacagGTGGTAGAACGTTTCCATGAACTGTTTGCCCAAACAAAGTATAAAGAAGCAGCTGAACTTGCTGCTGAGTCTCCGCAAGGAATCCTTCGCACACCTGATA
|| |||||| ||| | | | ||| | | | | || ||| | | | | | |||| || |||| || || || | || |||| ||||| |||||||| || || ||||| |||||||| || ||||||||||||||||| | ||| |
---------------------------gtaacgcttttat--cttcgatgatctttctctttgct--acctcttactgtatcgttctatgtgagt---agGTTGTGCAACGGTTTCAGGAGTTATTCCAACAAATGAAGTACAAAGAAGCTGCGGAGCTTGCAGCTGAGTCCCCTCAAGGAATCCTTCGCACGCATGACA
upper sequence: GLYMA18G02960.1 (Glycine max), 3'ss of exon 10
lower sequence: EFJ13237 (Selaginella moellendorffii), 3'ss of exon 10
gtgtgtaatagcctcatttaaaatggtttagtttttttattgctttgtttttttttgtgtgtattttactcattaacatgcctccttgttgacattacagGTGGTAGAACGTTTCCATGAACTGTTTGCCCAAACAAAGTATAAAGAAGCAGCTGAACTTGCTGCTGAGTCTCCGCAAGGAATCCTTCGCACACCTGATA
|| |||||| ||| | | | ||| | | | | || ||| | | | | | |||| || |||| || || || | || |||| ||||| |||||||| || || ||||| |||||||| || ||||||||||||||||| | ||| |
---------------------------gtaacccttttat--cttcgatgatctttctctttgct--acctcttactgtatcgttctatgtgagt---agGTTGTGCAACGGTTTCAGGAGTTATTCCAACAAATGAAGTACAAAGAAGCTGCGGAGCTTGCAGCTGAGTCCCCTCAAGGAATCCTTCGCACGCATGACA atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tgtttttttttgtgtgtattttactcattaacatgcctccttgttgacattacagGTGGTAGAACGTTTCCATGAACTGTTTGCCCAAACAAAGTATAAAGAAGCAGCTGAACTTGCTGCTGAGTCTCCGCAAGGAATCCTTCGCACACCTGATA
tattttactcattaa 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtgtgtaatagcctcatttaaaatggtttagtttttttattgctttgtttttttttgtgtgtattttactcattaacatgcctccttgttgacattacagGTGGTAGAACGTTTCCATGAACTGTTTGCCCAAACAAAGTATAAAGAAGCAGCTGAACTTGCTGCTGAGTCTCCGCAAGGAATCCTTCGCACACCTGATA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAA
gtgtgta
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - cctcctt