Sequence
atgc intronic sequence ATGC exonic sequence...tggtttatccatggaagacttttactacatgatgccttagtttccattctttgctataaatgattcatttattgttttcttgtgtgtgtgtctactctagACATTTGATGCTGTTGATGGGAAGCAAGCTAGACGAACAAATTCCTCAAGCCCATTGGGGGAGCTCTTTGATCATG
Basic information
species | Glycine max |
transcript | GLYMA12G08720.1 |
intron # | 5 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA12G08720.1 (Glycine max), 3'ss of exon 5
lower sequence: AT1G13560.2 (Arabidopsis thaliana), 3'ss of exon 4
tggtttatccatggaagacttttactacatgatgccttagtttccattctttgctataaatgattca-----tttattgttttcttgtgtgtgtgtctactctagACATTTGATGCTGTTGATGGGAAGCAAGCTAGACGAACAAATTCCTCAAGCCCATTGGGGGAGCTCTTTGATCATG
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--gtttgcgtctctctttttcttcaaaagtttaactttctgttatatgtgctggtgaaggtgttttgaagtcttttttatcttacaccttttgagcttttattagACATTTGATGCGGTTGATGGGAAGCAAGCAAGAAGGACAAATTCCTCTAGCCCCCTAGGAGAGCTCTTCGATCATG
upper sequence: GLYMA12G08720.1 (Glycine max), 3'ss of exon 5
lower sequence: AT3G25585.3 (Arabidopsis thaliana), 3'ss of exon 4
-------tggtttatccatggaagacttttactacatgatgccttagtttccattctttgctataaatgattcatttattgttttcttgtgtgtgtgtctactctagACATTTGATGCTGTTGATGGGAAGCAAGCTAGACGAACAAATTCCTCAAGCCCATTGGGGGAGCTCTTTGATCATG------------------------
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gtctgcttcttttttctatatcaacctaatttcatctgcttgttaagggtcatgtaatctgtcttcctgacatagttggtgcattgtcgagtgaat------tctagACATTTGATGCGGTTGATGGGAAGCAAGCACGAAGAACAAATTCATCTAGCCCACTAGGAGAGCTTTTTGACCATGGTTGCGATGCACTTGGCTGTGCGT
upper sequence: GLYMA12G08720.1 (Glycine max), 3'ss of exon 5
lower sequence: Vv01s0010g00950.t01 (Vitis vinifera), 3'ss of exon 5
tggtttatccatggaagacttttactacatgatgccttagtttccattctttgctataaatgatt-catttattgt-tttcttgtgtgtgtgtctactctagACATTTGATGCTGTTGATGGGAAGCAAGCTAGACGAACAAATTCCTCAAGCCCATTGGGGGAGCTCTTTGATCATG
| ||| || ||| | || || || | |||| |||||| | || |||| | || ||| || | | | | |||| |||||||||||||||||||||||||| || || ||||||||||| || |||||||| || || ||||| ||||
tttgctatgattgagtagtgtttcatttattatattttggcaat--gccttttctataatttctttcattcttggtattttttttccctaaaaacatgccagACTTTTGATGCTGTTGATGGGAAGCAAGCAAGGCGGACAAATTCCTCTAGTCCATTGGGAGAACTTTTTGACCATG
upper sequence: GLYMA12G08720.1 (Glycine max), 3'ss of exon 5
lower sequence: PP1S68_234V6.1 (Physcomitrella patens), 3'ss of exon 4
----tggtttatccatggaagacttttactacatgatgccttagtttccattctttgctataaatgattcatttattgttttcttgtgtgtgtgtctactctagACATTTGATGCTGTTGATGGGAAGCAAGCTAGACGAACAAATTCCTCAAGCCCATTGGGGGAGCTCTTTGATCATG
| | | | || ||| |||| | | || | | | ||| | | | | | | | ||||| | | | |||| ||||||||||||||||| ||||||||||| || ||||| || || ||||| | || ||||| |||||||| |
attgccgctcaccgatcattacgatttttcgagtgatttaaggggatgcagttctgcccatacac--ccaagtcagaatgtctcaatttgtgtattt--tacagACTTTTGATGCTGTTGATGGCAAGCAAGCTAGGCGGACAAACTCTTCGAGCCCTCTCGGAGAGCTTTTTGATCACG
upper sequence: GLYMA12G08720.1 (Glycine max), 3'ss of exon 5
lower sequence: PP1S269_30V6.1 (Physcomitrella patens), 3'ss of exon 5
-tggtttatc-catggaagacttttactacatgatgccttagtttccattctttgctataaatgattcatttattgttttcttgtgtgtgtgtctactctagACATTTGATGCTGTTGATGGGAAGCAAGCTAGACGAACAAATTCCTCAAGCCCATTGGGGGAGCTCTTTGATCATG
| | | || || ||| | ||| | | | | || || ||| | || | || | ||| | | |||| |||||||||||||||||||| |||||||| || |||||||| || || || | || || || |||||||| |
ataactagtggcagctgcgatatttctcaattgacggatatggatgcagcgttaattatccacccttaagatacggc--tctaaacccaatcttcttcacagACCTTTGATGCTGTTGATGGGAAACAAGCTAGGCGGACAAATTCGTCGAGTCCTCTTGGAGAACTTTTTGATCACG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.attctttgctataaatgattcatttattgttttcttgtgtgtgtgtctactctagACATTTGATGCTGTTGATGGGAAGCAAGCTAGACGAACAAATTCCTCAAGCCCATTGGGGGAGCTCTTTGATCATG
tctactct CT-rich tract
tataaatgattcattt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
tggtttatccatggaagacttttactacatgatgccttagtttccattctttgctataaatgattcatttattgttttcttgtgtgtgtgtctactctagACATTTGATGCTGTTGATGGGAAGCAAGCTAGACGAACAAATTCCTCAAGCCCATTGGGGGAGCTCTTTGATCATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGCT
- - - - ccatgga
- - - - - - - - - - - - - - -tgatgcc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -gtgtgtg