Sequence
atgc intronic sequence ATGC exonic sequencegtgagataattgtgtgaaattgtcttcctataggtttacacatactaattgaaagatgttctaaatctatacattacttgattagCCTTGCATCATTTTTATGGATGAGATCGATGCCATTGGAGGTCGCCGTTTCAGTGAGGGAACAAGTGCAGATCGTGAGATTCAGAGAACGCTAATGGAGC
Basic information
species | Glycine max |
transcript | GLYMA04G03180.1 |
intron # | 6 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA04G03180.1 (Glycine max), 3'ss of exon 6
lower sequence: Vv18s0001g13090.t01 (Vitis vinifera), 3'ss of exon 6
gtgagat----aattgtgtgaaat-tgtcttcctataggtttacacatactaattgaaagatgttctaaatc-tatacatt-acttgattagCCTTGCATCATTTTTATGGATGAGATCGATGCCATTGGAGGTCGCCGTTTCAGTGAGGGAACAAGTGCAGATCGTGAGATTCAGAGAACGCTAATGGAGC
|| ||| ||| |||||||| ||| ||||| | | | || || |||| | | || | | | || | || |||| ||||| ||||||||||||||||| |||||||| || || |||||||||||||||||||||||||| || ||||| || || ||||| || ||||||
gtaagagcttggattttgtgaaatatgtgttccttttttataatttatgtctatccaaagttaacgttgataatgtgcttttatttttcaagCCCTGCATTATTTTTATGGATGAGATTGATGCCATCGGTGGACGCCGTTTCAGTGAGGGAACAAGTGCTGACCGTGAAATACAAAGAACACTGATGGAGT
upper sequence: GLYMA04G03180.1 (Glycine max), 3'ss of exon 6
lower sequence: PP1S47_46V6.2 (Physcomitrella patens), 3'ss of exon 6
-----------------------------gtgagataattgtgtgaaattgtcttcctataggtttacacatactaattgaaagatgttctaaatct-----atacattacttgat-------tagCCTTGCATCATTTTTATGGATGAGATCGATGCCATTGGAGGTCGCCGTTTCAGTGAGGGAACAAGTGCAGATCGTGAGATTCAGAGAACGCTAATGGAGC
| || |||| || ||||| || | || || | | | || | |||||| | ||| ||| ||||| |||| ||||| || |||||||||||||| ||||| |||||||| || | || || || || |||||||||||||| |||||||| | || || ||||||
gtaattttcttctgcattcgtcttagatcttttcattattgagtattcccgtcttaacattgatt-actcttcaaaggtgcatcctgttctgagtcttgctgatatggcacttgtcgtttttgcagCCGTGCATAATATTTATGGATGAGATTGATGCAATTGGAGGACGTAGGTTTAGCGAAGGTACAAGTGCAGATCGAGAGATTCAACGCACACTCATGGAGT
upper sequence: GLYMA04G03180.1 (Glycine max), 3'ss of exon 6
lower sequence: PP1S13_419V6.1 (Physcomitrella patens), 3'ss of exon 6
---------------------------------------------------------gtgagataattgtgtgaaattgtctt-cctataggtttacacatactaattgaaagatgttctaaatctatac-attacttgattagCCTTGCATCATTTTTATGGATGAGATCGATGCCATTGGAGGTCGCCGTTTCAGTGAGGGAACAAGTGCAGATCGTGAGATTCAGAGAACGCTAATGGAGC
| | | || ||| ||| | ||| | | | | | | | || | | || |||| | ||||||||||||| |||||||||||||| |||||||||||||| || ||||| || ||||| || ||||||||||| || || ||| | || || ||||||
gtactacctcttttcatctgcacttggttcagttcttccatattaaagtggttacaggagttacgcttttgttttgttgattaacctccaaaactgctaacgttgttgttgtggtggctactttgtggaccattatctttgcagCCTTGCATCATATTTATGGATGAGATTGATGCCATTGGAGGCCGTCGTTTTAGCGAGGGTACTAGTGCAGATCGAGAAATCCAGCGTACCCTTATGGAGT
upper sequence: GLYMA04G03180.1 (Glycine max), 3'ss of exon 6
lower sequence: PP1S91_182V6.1 (Physcomitrella patens), 3'ss of exon 6
---------------------------------------gtgagataattgtgtgaaattgtcttcctatagg--tttacacatactaattgaaagatgttctaaatctatacattacttgatt-----agCCTTGCATCATTTTTATGGATGAGATCGATGCCATTGGAGGTCGCCGTTTCAGTGAGGGAACAAGTGCAGATCGTGAGATTCAGAGAACGCTAATGGAGC
|| || || ||| | ||| | | | ||| || | || | | | || | | ||| || || ||||||||||||||||||||||||| || ||||| || |||||||| || || || ||||| ||||| || ||||| || |||||| | ||||||||||||
gtaacgtctctccatctgaatttagttcatttcttttagactaggtagttacatgagttaagcttgatttcgtgttttgaacgtccttgtgcatacatcgttgtagtctgctaatgtgccaatctttacagCCTTGCATCATTTTTATGGATGAAATTGATGCGATCGGAGGTCGTCGGTTTAGCGAGGGTACAAGCGCTGATCGAGAAATTCAGCGGACGCTAATGGAGTMapped EST sequences
Showing partial alignments of ESTs and genomic sequences. See full alignments
ATGC EST sequence
ATGC genomic sequence (exon)
ATGC genomic sequence (truncated intron)
EST:
gi|208088440|gb|GD890728.1|GD890728EST: CACGTGATCACCAG CCTTGCATCATTTTTATGGATGAGATCGATGCCATTGGAGGTCGCCGTTTC
genomic: CACGTGATCACCAGgtgagataat ... acttgattagCCTTGCATCATTTTTATGGATGAGATCGATGCCATTGGAGGTCGCCGTTTC
EST:
gi|208336740|gb|GE136012.1|GE136012EST: AAAGTGCCAGGTTAATCAGAGAGATGTTTGGTTATGCACGTGATCACCAG CCTTGCATCATTTTTATGGATGAGATCGATGCCATTGGAGGTCGCCGTTTC
genomic: AAAGTGCCAGGTTAATCAGAGAGATGTTTGGTTATGCACGTGATCACCAGgtgagataat ... acttgattagCCTTGCATCATTTTTATGGATGAGATCGATGCCATTGGAGGTCGCCGTTTC
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.taggtttacacatactaattgaaagatgttctaaatctatacattacttgattagCCTTGCATCATTTTTATGGATGAGATCGATGCCATTGGAGGTCGCCGTTTCAGTGAGGGAACAAGTGCAGATCGTGAGATTCAGAGAACGCTAATGGAGC
taaatctatacatta 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtgagataattgtgtgaaattgtcttcctataggtttacacatactaattgaaagatgttctaaatctatacattacttgattagCCTTGCATCATTTTTATGGATGAGATCGATGCCATTGGAGGTCGCCGTTTCAGTGAGGGAACAAGTGCAGATCGTGAGATTCAGAGAACGCTAATGGAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAGAT