Sequence
atgc intronic sequence ATGC exonic sequence...attatccatagtcaccttcttggatctctgtacatgatttcaatagtcactagaagtctttgaaggttgcttctaactactcatttttcttatgaaatagGCCGTCAAACTTTCCTAAACACATCAAGGTGGATTGAAGAGGTGCGCATTGAGAGAGGCAGTGATGCTATTATTGTTCATGTTGGGAACAAAACTGACCT
Basic information
species | Glycine max |
transcript | GLYMA11G04340.1 |
intron # | 4 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA11G04340.1 (Glycine max), 3'ss of exon 4
lower sequence: GRMZM2G075719_T02 (Zea mays), 3'ss of exon 3
--------------------------------------------------------------------attatccatagtcacctt--cttggatctctgtacatgatttcaatagtcactagaagtctttgaaggttgcttctaactactcatttttcttatgaaatagGCCGTCAAACTTTCCTAAACACATCAAGGTGGATTGAAGAGGTGCGCATTGAGAGAGGCAGTGATGCTATTATTGTTCATGTTGGGAACAAAACTGACCT
||| ||| || | || ||| | | || | | || | || | ||| || |||| || | |||| | | ||| ||||| | || ||||| |||| ||||| | |||||| || || || |||| |||||| |||||||||| ||| ||||| | |||||||||||||||||||||
gtaatctctctctgtctctctcgcacacacaaacacacattctttaggaaaaaaaatggtatcagatgcacatcagtagcaacaatgactaggaagttt-tatcttttaaggattaaggacataaatttttactattttattcttacc-tttatttgtttcatgttgtagGCAGGCAGTCTTTCTTAAATACATCCAAGTGGATAGATGAAGTTCGCACTGAGAGGGGCAGTGATGTTATCATTGTGCTTGTTGGGAACAAAACTGACCT
upper sequence: GLYMA11G04340.1 (Glycine max), 3'ss of exon 4
lower sequence: GRMZM2G169694_T01 (Zea mays), 3'ss of exon 3
---------------------------------------------------------------attatccatagtcaccttcttggatctctgtacatgatttcaatagtca---ctagaagtctttgaaggttgcttctaactactcatttttcttatgaaatagGCCGTCAAACTTTCCTAAACACATCAAGGTGGATTGAAGAGGTGCGCATTGAGAGAGGCAGTGATGCTATTATTGTTCATGTTGGGAACAAAACTGACCT
| | | || | ||| |||| | || | | ||| | | | | || ||| || |||| ||| ||| | | ||| ||||| | || | ||| |||| ||||| | |||||| || || || |||| |||||| |||||||||| ||| ||||| | |||||||||||||||||||||
gtaatctccctctctcatacacacacattctatagaaatagttgttgtcagacgcacatcagtaacaacaatgactaggaacttatatcttt-taaa-ggtttaagcctttaaggacataaacttttactattttgttct---tacctttttgtttcatgttgtagGCAGGCAGTCCTTCTTAAATACATCTAAGTGGATAGAGGAAGTTCGCACTGAGAGGGGCAGTGATGTTATCATTGTGCTTGTTGGGAACAAAACTGACCT atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.gtcactagaagtctttgaaggttgcttctaactactcatttttcttatgaaatagGCCGTCAAACTTTCCTAAACACATCAAGGTGGATTGAAGAGGTGCGCATTGAGAGAGGCAGTGATGCTATTATTGTTCATGTTGGGAACAAAACTGACCT
ttctaac putative branch site (score: 1)
ctactcatttttctt CT-rich tract
atttttcttatgaaat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
attatccatagtcaccttcttggatctctgtacatgatttcaatagtcactagaagtctttgaaggttgcttctaactactcatttttcttatgaaatagGCCGTCAAACTTTCCTAAACACATCAAGGTGGATTGAAGAGGTGCGCATTGAGAGAGGCAGTGATGCTATTATTGTTCATGTTGGGAACAAAACTGACCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGAGG
- - - - - - caccttc
- - - - - - - - - - - - -ctctgta
- - - - - - - - - - - - - - - - catgatt
- - - - - - - - - - - - - - - - - - - - - - - - - - - -gtctttg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tgcttct