Sequence
atgc intronic sequence ATGC exonic sequence...tcaattccttttaaaggaactcattctctgttccctgatttgtgtttcacacttctatcctttattttcctaatttttacgaggcttgcatataatgcagACAGTGGATAATGACCTTGCATTGAAAATTTATATTAAAGCTAGAGCCACACCAAAAGTTGTTGCAGCTTTTGCGGAGAGGAGGGAATTTGATAAGATCC
Basic information
species | Glycine max |
transcript | GLYMA11G06720.1 |
intron # | 12 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA11G06720.1 (Glycine max), 3'ss of exon 12
lower sequence: LOC_Os11g01380.1 (Oryza sativa), 3'ss of exon 12
-tcaattccttttaaaggaactcattctctgttc-cctgatttgtgtttcacacttctatcctttattttcctaattttta------cgaggcttgca---tataatgcagACAGTGGATAATGACCTTGCATTGAAAATTTATATTAAAGCTAGAGCCACACCAAAAGTTGTTGCAGCTTTTGCGGAGAGGAGGGAATTTGATAAGATCC
| || | | | ||| | || || | | || |||| ||| | | || | | || ||| || || | |||| | | || |||| ||||| ||||| ||||| ||||||| || || || ||||| || || || ||||||||||| |||||||| || || ||||||||||| |||||||
gtaaaatgggtgttaagttgtttgttgattgcacatatcgattttgttacactgtgtcctgtttgactgtctggattgttcattaattgatacctgcactctttggtgtagACTGTGGACAATGATCTTGCTCTGAAAATATACATAAAGGCTAGGGCAACCCCTAAAGTTGTTGCCGCTTTTGCTGAAAGAAGGGAATTTGACAAGATCC
upper sequence: GLYMA11G06720.1 (Glycine max), 3'ss of exon 12
lower sequence: LOC_Os12g01390.1 (Oryza sativa), 3'ss of exon 12
-tcaattccttttaaaggaactcattctctgttc-cctgatttgtgtttcacacttctatcctttattttcctaattttta------cgaggcttgca---tataatgcagACAGTGGATAATGACCTTGCATTGAAAATTTATATTAAAGCTAGAGCCACACCAAAAGTTGTTGCAGCTTTTGCGGAGAGGAGGGAATTTGATAAGATCC
| || | | | ||| | || || | | || |||| ||| | | || | | || ||| || || | |||| | | || |||| ||||| ||||| ||||| ||||||| || || || ||||| || || || ||||||||||| |||||||| || || ||||||||||| |||||||
gtaaaatgggtcttaagttgtttgttgattgcacatatcgattttgttacactgtgtcctgtttgactgtctggattgttcattaattgatacctgcactctttggtgtagACTGTGGACAATGATCTTGCTCTGAAAATATACATAAAGGCTAGGGCAACCCCTAAAGTTGTTGCCGCTTTTGCTGAAAGAAGGGAATTTGACAAGATCC
upper sequence: GLYMA11G06720.1 (Glycine max), 3'ss of exon 12
lower sequence: GRMZM2G430947_T01 (Zea mays), 3'ss of exon 1
tcaattccttttaaaggaactcattctctgttccctgatttgtgtttcacacttctatcc-tttattttcctaatttttacgaggcttgcata---taatgcagACAGTGGATAATGACCTTGCATTGAAAATTTATATTAAAGCTAGAGCCACACCAAAAGTTGTTGCAGCTTTTGCGGAGAGGAGGGAATTTGATAAGATCC
| | | | | | || | | | | || | | || || | |||| | | ||| | | | || | | ||| |||| ||||| ||||| |||||| ||||||| || || || ||||| || || || ||||||||||| |||||||| || |||||||| ||||| |||| |
----tgtcataccgtgtttgttgatgcatggatcttactatactttgccaatttacattcacttatgtattggttgtttgctaagtgtgtgcacttttatgtagACTGTGGACAATGATCTTGCACTGAAAATATACATAAAGGCTAGGGCAACCCCTAAAGTTGTTGCTGCTTTTGCTGAAAGGAGGGAGTTTGACAAGACAC
upper sequence: GLYMA11G06720.1 (Glycine max), 3'ss of exon 12
lower sequence: GRMZM2G057576_T02 (Zea mays), 3'ss of exon 10
-tcaattccttttaaaggaactcattctctgttccctgatttgtgtt---tcacacttctat-cctttattttc-ctaatttttacgaggcttgcatataatgcagACAGTGGATAATGACCTTGCATTGAAAATTTATATTAAAGCTAGAGCCACACCAAAAGTTGTTGCAGCTTTTGCGGAGAGGAGGGAATTTGATAAGATCC
| | | | | | | | | || ||| || |||| | ||| || | | ||| || || ||||| || | | | | |||| ||||| ||||| |||||| ||||||| || || || || || || || || ||||||||||| |||||||| || |||||||| ||||| || || |
gtaagatgggtcctatgctgtttttattgattttactgtattttgttaaattacatttatttgtcttggttatcgctaatcatttcttgtaccctttgatgtatagACTGTGGACAATGATCTTGCACTGAAAATATACATCAAGGCCAGGGCAACCCCTAAAGTTGTTGCTGCTTTTGCTGAAAGGAGGGAGTTTGACAAAATAC
upper sequence: GLYMA11G06720.1 (Glycine max), 3'ss of exon 12
lower sequence: Vv06s0004g06860.t01 (Vitis vinifera), 3'ss of exon 12
tcaattccttttaaaggaactcattct--ctgttccctgat-ttgtgtttcacacttctatcctttattttcctaatttttacgaggct-----tgcatataatgcagACAGTGGATAATGACCTTGCATTGAAAATTTATATTAAAGCTAGAGCCACACCAAAAGTTGTTGCAGCTTTTGCGGAGAGGAGGGAATTTGATAAGATCC
||| |||||| ||| ||| | || | ||||| | | | ||| || ||| | | ||| || | | ||| | | || |||| |||||||||||||||||| ||||||| ||||| |||||||| ||||| ||||||||||||||||| ||||| ||||||||||| || ||||| || |
------acttggaaaggagtatggtctaatagttttttcatgctctgtttgatttgtgtttcccttccttt--tggtctttctgatgttgtaattgctaacattgtagACGGTGGATAATGACCTTGCACTGAAAATATATATCAAAGCTAGGGCCACTCCAAAAGTTGTTGCAGCATTTGCTGAGAGGAGGGAGTTCGATAAAATTC atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ttcacacttctatcctttattttcctaatttttacgaggcttgcatataatgcagACAGTGGATAATGACCTTGCATTGAAAATTTATATTAAAGCTAGAGCCACACCAAAAGTTGTTGCAGCTTTTGCGGAGAGGAGGGAATTTGATAAGATCC
tcctaat putative branch site (score: 2)
tttattttcctaattt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
tcaattccttttaaaggaactcattctctgttccctgatttgtgtttcacacttctatcctttattttcctaatttttacgaggcttgcatataatgcagACAGTGGATAATGACCTTGCATTGAAAATTTATATTAAAGCTAGAGCCACACCAAAAGTTGTTGCAGCTTTTGCGGAGAGGAGGGAATTTGATAAGATCC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGGAG
-caattcc
- - - - - - - - - - -cattctc
- - - - - - - - - - - - - - - ttccctg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -gcttgca