Sequence
atgc intronic sequence ATGC exonic sequence...aatgggtattatgaaataatttaagcagagtagtttgaacactgaaacttggtcaataatttgttcatgtgagtaaaatttactctactaaattgtgcagGCGATGATTGCGTCTCTATACAAACTGGTTGCTCGGACATATATGTACACAATGTGAATTGTGGACCTGGTCATGGAATCAGCATTGGAAGTCTTGGCAG
Basic information
species | Glycine max |
transcript | GLYMA19G00230.1 |
intron # | 4 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA19G00230.1 (Glycine max), 3'ss of exon 4
lower sequence: LOC_Os01g45060.1 (Oryza sativa), 3'ss of exon 5
------aatgggtattatgaaat-aatttaagcagagtagtttgaacactgaaacttggtcaataatttgttcatgtgagtaaaatttactctactaaattgtgcagGCGATGATTGCGTCTCTATACAAACTGGTTGCTCGGACATATATGTACACAATGTGAATTGTGGACCTGGTCATGGAATCAGCATTGGAAGTCTTGGCAG
| | ||| | || || || | |||| || ||| | || | | ||| | || ||| ||| || | || | |||||| ||||| |||||||| || ||||| || ||| | ||| || ||||||||||||||||||||||||| |||||||||||||||||| | || ||| |
aaacttcaagagtactgaactatgaagctatcttttgcagtt-actcaacaaaagcagaaaaaca--tagttaacatg--taatttttggtcgaata--tgatgcagGTGATGACTGCGTCTCCATTCAAACAGGATGCAGCAATATAAATATACACAATGTGAATTGTGGACCTGGCCATGGAATCAGCATTGGAGGCCTAGGCCG
upper sequence: GLYMA19G00230.1 (Glycine max), 3'ss of exon 4
lower sequence: LOC_Os01g44970.1 (Oryza sativa), 3'ss of exon 5
------aatgggtattatgaaat-aatttaagcagagtagtttgaacactgaaacttggtcaataatttgttcatgtgagtaaaatttactctactaaattgtgcagGCGATGATTGCGTCTCTATACAAACTGGTTGCTCGGACATATATGTACACAATGTGAATTGTGGACCTGGTCATGGAATCAGCATTGGAAGTCTTGGCAG
| | ||| | || || || | |||| || ||| | || | | ||| | || | ||| | || || |||||| ||||| |||||||| || ||||| || ||| | ||| || ||||||||||||||||||||||||| |||||||||||||||||| | || ||| |
aaacttcaagagtactgaactatgaagctatcttttgcagtt-actcaacaaaagcagaaaaaca--tagttaacatgtat----tttttggtcgtatatgatgcagGTGATGACTGCGTCTCCATTCAAACAGGATGCAGCAATATAAATATACACAATGTGAATTGTGGACCTGGCCATGGAATCAGCATTGGAGGCCTAGGCCG
upper sequence: GLYMA19G00230.1 (Glycine max), 3'ss of exon 4
lower sequence: GRMZM2G037431_T01 (Zea mays), 3'ss of exon 5
aatgggtattatgaaataatttaagcagagtagtttgaacactgaaacttggtcaataatttgtt-catgtgagtaaaat-ttactctactaaatt--gtgcagGCGATGATTGCGTCTCTATACAAACTGGTTGCTCGGACATATATGTACACAATGTGAATTGTGGACCTGGTCATGGAATCAGCATTGGAAGTCTTGGCAG
|| | || | | | | || |||| | | | | | | || || | | || | || || || | ||| |||||| ||||||||| |||| || || || || ||| ||||| || ||||||| |||||||||||||| || |||||||||||||| || | || ||| |
cctgtaaaccctgca----tgtcaaaggacatgtttcagagttaagagtacactgaaaaactgctgtaaactagcataacattcctttgtcctattcgatgcagGTGATGATTGCATCTCCATCCAGACAGGATGCAGCAACATAAATATACACAACGTGAATTGTGGACCAGGCCATGGAATCAGCATAGGTGGACTAGGCCG
upper sequence: GLYMA19G00230.1 (Glycine max), 3'ss of exon 4
lower sequence: GRMZM2G179696_T03 (Zea mays), 3'ss of exon 5
aatgggtattatgaaataatttaagcagagtagtttgaacactgaaacttggtcaataatttgttc----atgtgagtaaaatttactctactaaattgtgcagGCGATGATTGCGTCTCTATACAAACTGGTTGCTCGGACATATATGTACACAATGTGAATTGTGGACCTGGTCATGGAATCAGCATTGGAAGTCTTGGCAG
||| || | || | || | || |||| | | | ||| | || || | | | | | | | | | ||| |||||| || |||||| |||| || || || || ||| ||||| || |||| || |||||||||||||| || |||||||||||||| || | || ||| |
catgtatactctgca----cttcaaaggacatgtttcagagttaagactacactgaaaaactgctgtggagtatcataacatcgttttgtcctattcgatgcagGTGACGATTGCATCTCCATCCAGACAGGATGCAGCAACATAAATATACATAACGTGAATTGTGGACCAGGCCATGGAATCAGCATAGGTGGACTAGGCCG
upper sequence: GLYMA19G00230.1 (Glycine max), 3'ss of exon 4
lower sequence: Vv14s0066g01060.t01 (Vitis vinifera), 3'ss of exon 5
--------------------------------------------------------------------aatgggtattatgaa-ataatttaagcagagtagt--ttgaacactga--aacttggtcaata-----atttgttcatgtgagtaaaatttactc-tactaaattgtgcagGCGATGATTGCGTCTCTATACAAACTGGTTGCTCGGACATATATGTACACAATGTGAATTGTGGACCTGGTCATGGAATCAGCATTGGAAGTCTTGGCAG
| | || || | ||| || ||| | | | || || | || ||||||| | || | | ||||| || |||| || | ||| | |||| || || || || || ||||| || || ||||| | |||| ||||||||||||||||||||||||||||||||||||||||||||| |||| || ||
gtaaatccaaaaaccttaaaagtcttgcgacttgtccttttgagaacacaagcaccacggctggtcatttttgctagtagaagcgtaacttgcgcaaaattatggcagagtcctcacaaaattggtcatcattgacatctaagttcatcagtaacgttaactcataatgcattctacagGAGACGACTGTGTATCAATACAGACAGGATGCTCAAATATATTCGTACACAATGTGAATTGTGGACCTGGTCATGGAATCAGCATTGGAGGTCTAGGGAG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.aacttggtcaataatttgttcatgtgagtaaaatttactctactaaattgtgcagGCGATGATTGCGTCTCTATACAAACTGGTTGCTCGGACATATATGTACACAATGTGAATTGTGGACCTGGTCATGGAATCAGCATTGGAAGTCTTGGCAG
tactaaa putative branch site (score: 1)
taaaatttactctact 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
aatgggtattatgaaataatttaagcagagtagtttgaacactgaaacttggtcaataatttgttcatgtgagtaaaatttactctactaaattgtgcagGCGATGATTGCGTCTCTATACAAACTGGTTGCTCGGACATATATGTACACAATGTGAATTGTGGACCTGGTCATGGAATCAGCATTGGAAGTCTTGGCAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAAG
- - - - - - - - - - - - - - - - - - - -cactgaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tcatgtg