Sequence
atgc intronic sequence ATGC exonic sequence...cttgttcttttaacttatcatttctctctaatgaactcttgttgtatagagaaaaaggatatctgtctgattctttcccatttatttatgtgtctactagAGGGACAAAATTGAGGAAGCTTTAAGGCTGGCAGAGCTATCAGCTGAGAAGCCTCATTTTTCACATTGTCTAGAGTGGCTTCTTTTTACAGTATTTGAAG
Basic information
species | Glycine max |
transcript | GLYMA18G47050.1 |
intron # | 12 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA18G47050.1 (Glycine max), 3'ss of exon 12
lower sequence: GRMZM2G052750_T02 (Zea mays), 3'ss of exon 11
cttgttcttttaacttatcatttctctctaatgaactcttgttgtatagagaaaaag----gatatctgtctgattctttcccatttatttat-gtgtctactagAGGGACAAAATTGAGGAAGCTTTAAGGCTGGCAGAGCTATCAGCTGAGAAGCCTCATTTTTCACATTGTCTAGAGTGGCTTCTTTTTACAGTATTTGAAG
| || | | | || | | | | ||| ||| | || || | || || | || || | | | || || || | || |||||||||| ||||| |||||||| | ||||| | | ||||| || || ||||| || || || ||||||||||||||||| |||||||||||||| |
----tgctctgagatcattctcaaattttgttttga-cttattggcttgaaaacattttctgacgcctctaaatttaattatcctatgttaattgtttaaaccagAGGGACAAGATTGATGAAGCTTTGCGCTTGGCAAATTTGTCAGCAGAAAAACCTCACTTCTCTCACTGTCTAGAGTGGCTTCTGTTTACAGTATTTGATG
upper sequence: GLYMA18G47050.1 (Glycine max), 3'ss of exon 12
lower sequence: GRMZM2G475867_T01 (Zea mays), 3'ss of exon 11
cttgttcttttaacttatcatttctctctaatgaactcttgttgtatagagaaaaag-gatatctgtctgattctttcccatttatttat-gtgtctactagAGGGACAAAATTGAGGAAGCTTTAAGGCTGGCAGAGCTATCAGCTGAGAAGCCTCATTTTTCACATTGTCTAGAGTGGCTTCTTTTTACAGTATTTGAAG
|| | | | | | | | | | ||| | ||| |||| | | | || | || | | || | | | || || || | || |||||||||| ||||| || ||||| ||||| | | || || || || |||||||| || || ||| ||||||||||||| |||||||||||||| |
-gtgctgtgctgctctgcc-tcaatttttgttgacttattggtgtaaacacattttctgacacctctaaattcaattatcctatgttaattgtttaaaccagAGGGACAAGATTGAAGAGGCTTTGCTCTTGGCAAATTTGTCCGCAGAAAAACCTCATTTCTCTCACTGTTTAGAGTGGCTTCTGTTTACAGTATTTGATG
upper sequence: GLYMA18G47050.1 (Glycine max), 3'ss of exon 12
lower sequence: Vv15s0046g01890.t01 (Vitis vinifera), 3'ss of exon 12
cttgttcttttaacttatcatttctctctaatgaactcttgttgtatagagaaaaaggatatctgtct-gattctt--tcccatttat--ttatgtgtctactagAGGGACAAAATTGAGGAAGCTTTAAGGCTGGCAGAGCTATCAGCTGAGAAGCCTCATTTTTCACATTGTCTAGAGTGGCTTCTTTTTACAGTATTTGAAG
|| | || || |||| || | || || | ||| || | ||| | ||| | | | ||| | || ||| | || |||||||||| | |||||||| ||| | ||||| | ||||||| ||||||||||||||||| |||||||| ||||||||||||||||| |||||||| |
--tgcattcgtactcaat--tttcatcttaggtagtagatgctg-acagaaaattctattgctattctaggttcctaattctgtttctaattttgtatacaccagAGGGACAAGAGCGAGGAAGCATTACGTTTGGCACAATTATCAGCAGAGAAGCCTCATTTTTCCCATTGTCTGGAGTGGCTTCTTTTTACTGTATTTGATG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.atagagaaaaaggatatctgtctgattctttcccatttatttatgtgtctactagAGGGACAAAATTGAGGAAGCTTTAAGGCTGGCAGAGCTATCAGCTGAGAAGCCTCATTTTTCACATTGTCTAGAGTGGCTTCTTTTTACAGTATTTGAAG
gtctgat putative branch site (score: 4)
atttatttatgtgt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
cttgttcttttaacttatcatttctctctaatgaactcttgttgtatagagaaaaaggatatctgtctgattctttcccatttatttatgtgtctactagAGGGACAAAATTGAGGAAGCTTTAAGGCTGGCAGAGCTATCAGCTGAGAAGCCTCATTTTTCACATTGTCTAGAGTGGCTTCTTTTTACAGTATTTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGAAG
cttgttc
- - - - - - - - - - - - - - -aatgaac
- - - - - - - - - - - - - - - - - - -cttgttg
- - - - - - - - - - - - - - - - - - - - - - - - -agaaaaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ctgtctg