Sequence
atgc intronic sequence ATGC exonic sequence...attgcttccatattcttattgatgatgatagatctggaacaccttacaactacaatgttctggtccctttcctcttaatcattgtacctaacaataaaagTGCTGATTTTGCCTATATTTGAAGGAACCGTACCTCTTCCGTGGTCCAACAGGATTAAGATTGCCCTTGGTGCAGCAAAAGGATTGGCCTTCCTCCATAA
Basic information
species | Glycine max |
transcript | GLYMA13G22790.1 |
intron # | 3 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA13G22790.1 (Glycine max), 3'ss of exon 3
lower sequence: GRMZM2G410191_T02 (Zea mays), 3'ss of exon 7
attgcttccatattcttattgatgatgatagatctggaacacctta-caactacaatgttctggtccctttcctcttaatcattgtacctaacaataaaagTGCTGATTTTGCCTATATTTGAAGGAACCGTACCTCTTCCGTGGTCCAACAGGATTAAGATTGCCCTTGGTGCAGCAAAAGGATTGGCCTTCCTCCATAA------------------------
||||| | | || || | ||| |||| | ||| || | | ||||| || ||| || || | |||| || ||||||| ||| | || || || |||||||||||||| |||||||| || ||||| || |||||| | ||||||||||||
------------acaaagttgattttattttatgtgcctaatcttgtcaaccataatctttctacctgctcgttctta-----tgatcctgtcat--------cttactttgtttaatcttgaagGGACCCTTCCCCTACCTTGGTCCAACAGGATGAAGATTGCTCTAGGTGCCGCGAAAGGACTAGCCTTCCTCCATGGAGGTCCCAAACATGTTATTTACAG
upper sequence: GLYMA13G22790.1 (Glycine max), 3'ss of exon 3
lower sequence: GRMZM2G014596_T01 (Zea mays), 3'ss of exon 3
attgcttccatattcttattgatgatgatagatctggaacaccttacaactacaatgttctggtccctttcctcttaatcattgtacctaacaataaaagTGCTGATTTTGCCTATATTTGAAGGAACCGTACCTCTTCCGTGGTCCAACAGGATTAAGATTGCCCTTGGTGCAGCAAAAGGATTGGCCTTCCTCCATAA------------------------
| | | || || | || || | | |||| | ||| || || | ||||| || ||| || || | |||| || ||||||| | | || || || |||||||||||||| ||||||| || ||||| || |||||| | ||||||||||||
--------aaaagttgattttatttttatgtgcctaat---cttgtcaaccataatctttctatctgctcgttctta-----tgatcctgtcat--------cttactttgtttaatcttgaagGGGCTCTTCCCCTACCTTGGTCCAACAGGATGAAGATTGTTCTAGGTGCCGCGAAAGGAGTAGCCTTCCTCCATGGAGGTCCCAAACCTGTTATTTACAG
upper sequence: GLYMA13G22790.1 (Glycine max), 3'ss of exon 3
lower sequence: Vv11s0016g05720.t01 (Vitis vinifera), 3'ss of exon 3
attgcttccatattcttattgatgatgatagatctggaacaccttacaactacaatgttctggtccctttcctcttaatcattgtacctaacaataaaagTGCTGATTTTGCCTATA--TTTGAAGGAACCGTACCTCTTCCGTGGTCCAACAGGATTAAGATTGCCCTTGGTGCAGCAAAAGGATTGGCCTTCCTCCATAA------------------------
|| ||||| | |||| || | | |||| | || | || | ||| | | | | ||| | ||||||| || || | ||||||| ||| |||||||||| ||||||||||||||||||||||| ||||||||||||||||| ||||||| ||||| |
-----------ttttttattcagtatgacag-----------cccatttctactctttttaaaa----tggaactaattcactttgtgttatcatacatatgctgatgttatctcaaatcttgaagGGACCATACCTCTTCCATGGTCCAACAGGATTAAGATTGCACTTGGTGCAGCAAAAGGGCTGGCCTTTCTCCACGAGGGTCCTGAACCTGTTATTTACAG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.acaactacaatgttctggtccctttcctcttaatcattgtacctaacaataaaagTGCTGATTTTGCCTATATTTGAAGGAACCGTACCTCTTCCGTGGTCCAACAGGATTAAGATTGCCCTTGGTGCAGCAAAAGGATTGGCCTTCCTCCATAA
acctaac putative branch site (score: 2)
taacaataaaa 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
attgcttccatattcttattgatgatgatagatctggaacaccttacaactacaatgttctggtccctttcctcttaatcattgtacctaacaataaaagTGCTGATTTTGCCTATATTTGAAGGAACCGTACCTCTTCCGTGGTCCAACAGGATTAAGATTGCCCTTGGTGCAGCAAAAGGATTGGCCTTCCTCCATAA
- tgcttcc
- - - - - - - - - - gatgatg
- - - - - - - - - - - - - - - - - - - - -ccttaca