Sequence
atgc intronic sequence ATGC exonic sequencegtaatccctataacaataaattcaacaatggaattgaccataaaatttatgtgtgaattgttaattgataattatctaatttcaaaaatataatccaccagTTTGTGGCTGCTACTCAACCAATCAATTCATTAGCCTTTGTATTTGATGGAGTGAACTATGGAGCTTCTGATTTTGCATATTCAGCATACTCTCTGGCAA
Basic information
species | Glycine max |
transcript | GLYMA13G27300.1 |
intron # | 11 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA13G27300.1 (Glycine max), 3'ss of exon 11
lower sequence: LOC_Os10g13940.1 (Oryza sativa), 3'ss of exon 9
-------------------------------------------------------------------------------------gtaatccctataaca-ataaattcaacaatggaattgaccataaaatttatgtgtgaattgttaattgataattatctaatttcaaaaatataatccac---cagTTTGTGGCTGCTACTCAACCAATCAATTCATTAGCCTTTGTATTTGATGGAGTGAACTATGGAGCTTCTGATTTTGCATATTCAGCATACTCTCTGGCAA
| | ||| || | || | | || || | | | | ||| || |||| || | || | ||| | | | ||| | | |||||||| || ||||||||||||||| | ||||| ||||| |||||||| | || |||||||| || ||||||| |||| | || || || ||
gtaaactttctttatactgatgccaaaataattacaattttaagtcatattgtagttaggattcctcagttgtgtgcgggagcctgatgttcctttatgatatctttcctactgtgcattgggatgcctgcctactgtcaga---gttacctggaatttttttaactaaagagttatttttcctgttcagTTTGTCTCTCTGACTCAACCAATCAATGCGTTAGCTTTTGTTTTTGATGGTATCAATTATGGAGCATCAGATTTTGGATATGCTGCTTATTCAATG----
upper sequence: GLYMA13G27300.1 (Glycine max), 3'ss of exon 11
lower sequence: Vv13s0064g00930.t01 (Vitis vinifera), 3'ss of exon 10
gtaatccctataacaataaattcaacaatggaattgaccataaaattt-atgtgtgaa--ttgttaattgataattatct-aatttcaaaaatataatccaccagTTTGTGGCTGCTACTCAACCAATCAATTCATTAGCCTTTGTATTTGATGGAGTGAACTATGGAGCTTCTGATTTTGCATATTCAGCATACTCTCTGGCAA
|| || | || ||| ||| || ||| | ||| | ||| |||| || || |||| | || ||| || || || | | | || ||||| | || || || ||||||||||||| ||||||||||| || ||||||||||||| |||||| || |||||||||||| | |||||||| ||
--aaaaactgttttaaaaaa--caattatcaaatcaaacattattttttatgtttgctcttttttaactcattcttaactcaaatttttggctttcgactac-agTTTATCGCGGCGACCCAACCAATCAATTGCTTAGCCTTTGTTTTCGATGGAGTGAACTTTGGAGCATCGGATTTTGCATATACTGCATACTCCATG----
upper sequence: GLYMA13G27300.1 (Glycine max), 3'ss of exon 11
lower sequence: Vv13s0064g00940.t01 (Vitis vinifera), 3'ss of exon 11
gtaatccctataacaataaattcaacaatggaattgaccataaaatttatgtgtgaattgttaattgataattatctaatttcaaaaatataatccaccagTTTGTGGCTGCTACTCAACCAATCAATTCATTAGCCTTTGTATTTGATGGAGTGAACTATGGAGCTTCTGATTTTGCATATTCAGCATACTCTCTGGCAA
||| || ||| | | | || || || | | | ||| || | | | || ||| | ||| || | | | || ||||||| ||||| |||||||| || ||||| || |||||||| || || || ||||||| |||||| || |||||||||||||| |||||||| ||
gtatgtcccatatcta-atatgcattt------ttttcttttcattttttgagctcacgatcaactga--aatatttaccctt----ttgtgat--gatagTTTGTTGCTGCAACTCAACCGATAAATTCTTTGGCCTTTGTCTTCGACGGCGTGAACTTTGGAGCATCGGATTTTGCATATTCTGCATACTCCATG----
upper sequence: GLYMA13G27300.1 (Glycine max), 3'ss of exon 11
lower sequence: PP1S88_225V6.1 (Physcomitrella patens), 3'ss of exon 10
----gtaatccctataacaataaattcaacaatggaattgaccataaaatttatgtgtgaattgttaattgataattatctaatttcaaaaatataatccaccagTTTGTGGCTGCTACTCAACCAATCAATTCATTAGCCTTTGTATTTGATGGAGTGAACTATGGAGCTTCTGATTTTGCATATTCAGCATACTCTCTGGCAA
| | | | | | || | || ||| || || | ||| | | | | | ||| | | | ||| | | | | | |||||||||||| |||||||||||||| |||||||| ||||| |||||||| | | |||||||| || || ||| | ||| | || ||||| ||
tgtggcatcgcgtgtgccgatgaggtctcttatg----cgagcaaagaatccagcaataagtaaatg-ttgtttttgagataacgttggtgctgttacactgcagTTTGTGGCTCTAACTCAACCAATCAACTCATTAGCATTTGTCTTTGATGGCATTCATTATGGAGCGTCAGACTTTCCTTATGCTGCTTACTCAATG---- atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ttatgtgtgaattgttaattgataattatctaatttcaaaaatataatccaccagTTTGTGGCTGCTACTCAACCAATCAATTCATTAGCCTTTGTATTTGATGGAGTGAACTATGGAGCTTCTGATTTTGCATATTCAGCATACTCTCTGGCAA
atctaat putative branch site (score: 3)
aattgttaattgataa 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaatccctataacaataaattcaacaatggaattgaccataaaatttatgtgtgaattgttaattgataattatctaatttcaaaaatataatccaccagTTTGTGGCTGCTACTCAACCAATCAATTCATTAGCCTTTGTATTTGATGGAGTGAACTATGGAGCTTCTGATTTTGCATATTCAGCATACTCTCTGGCAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGCTT