Sequence
atgc intronic sequence ATGC exonic sequence...ggctttggatcattatcattgtgtttaggattgtaaaaattctgaaacaagcttagctttgtttactgcaagacggataaaattcatcttatgtgaacagGTCTTGGCCATTGAGGAGGTCTTCAAGAATAGGGTGACAAATGTAGTGTTTATGGGAATGGGTGAACCAATGTTAAACCTGAAGGCAGTACTTGAAGCAC
Basic information
species | Glycine max |
transcript | GLYMA02G41500.1 |
intron # | 5 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA02G41500.1 (Glycine max), 3'ss of exon 5
lower sequence: LOC_Os01g74190.1 (Oryza sativa), 3'ss of exon 5
ggctttggatcattatcattgtgtttaggattgtaaaaattctgaaacaagcttagctttgttta---ctgcaagacggataaaattcatcttatgtgaacagGTCTTGGCCATTGAGGAGGTCTTCAAGAATAGGGTGACAAATGTAGTGTTTATGGGAATGGGTGAACCAATGTTAAACCTGAAGGCAGTACTTGAAGCAC
||| || | | ||| | | || ||| ||| | | | || || |||| || ||| || | ||| || ||||| |||||||| |||||| ||| | | |||||||||||||||||||| ||||| |||||||| || ||||| |||||||| |||| | || ||||
---gttgtctctccacaacc-cacctagtacagcgtttatgtacaaaaaagataaattgtgcttgttcttgcacaacagattaatat--tctggcgttg-cagGTTTTGGCCATAGAGGAGACGTTCCAACACAGGGTGACAAATGTAGTGTTCATGGGGATGGGTGAGCCTATGTTGAACCTGAAATCAGTTTTAGAGGCAC
upper sequence: GLYMA02G41500.1 (Glycine max), 3'ss of exon 5
lower sequence: GRMZM2G168412_T01 (Zea mays), 3'ss of exon 4
-ggctttggatcattatcattgtgtttaggattgtaaaaattctgaaacaagcttagctttgtttactgcaagacggataaaattcatcttatgtga--acagGTCTTGGCCATTGAGGAGGTCTTCAAGAATAGGGTGACAAATGTAGTGTTTATGGGAATGGGTGAACCAATGTTAAACCTGAAGGCAGTACTTGAAGCAC
| || | || || | |||| | | || || | ||| | |||| || | | | | | | | || ||||| | ||||| |||||||| |||||| ||||| | |||||||||||||| ||||| ||||| |||||||| || ||| | ||||| ||| |||| || |||||||
gaaccttcaaccac-atgagattgttgaacag-gtcctccctcagcaacccctctgtctttcttcatccctcaatgca-acgttaaatattatgccattgcagGTGTTGGCCATCGAGGAGACGTTCAAACACAGGGTGACAAATGTTGTGTTCATGGGGATGGGTGAGCCCATGATGAACCTCAAGTCAGTTCTAGAAGCAC
upper sequence: GLYMA02G41500.1 (Glycine max), 3'ss of exon 5
lower sequence: GRMZM2G168412_T02 (Zea mays), 3'ss of exon 5
ggctttggatcattatcattgtgtttaggattgtaaaaattctgaaacaagcttagctttgtttactgcaagacggataaaattcatcttatgtga--acagGTCTTGGCCATTGAGGAGGTCTTCAAGAATAGGGTGACAAATGTAGTGTTTATGGGAATGGGTGAACCAATGTTAAACCTGAAGGCAGTACTTGAAGCAC
|| || | ||| | |||| || | | | | | | | || ||||| | ||||| |||||||| |||||| ||||| | |||||||||||||| ||||| ||||| |||||||| || ||| | ||||| ||| |||| || |||||||
--------------------------------gtcctccctcagcaacccctctgtctttcttcatccctcaatgca-acgttaaatattatgccattgcagGTGTTGGCCATCGAGGAGACGTTCAAACACAGGGTGACAAATGTTGTGTTCATGGGGATGGGTGAGCCCATGATGAACCTCAAGTCAGTTCTAGAAGCAC
upper sequence: GLYMA02G41500.1 (Glycine max), 3'ss of exon 5
lower sequence: AT2G39670.1 (Arabidopsis thaliana), 3'ss of exon 5
ggctttggatcatt---atcattgtgtttaggatt----gtaaaaattctgaaacaagcttagctttgtttactgcaagacggataaaattcatcttatgtgaacagGTCTTGGCCATTGAGGAGGTCTTCAAGAATAGGGTGACAAATGTAGTGTTTATGGGAATGGGTGAACCAATGTTAAACCTGAAGGCAGTACTTGAAGCAC
|| | | || | | || |||| || || |||||| | || | | || | || | || | || || || |||| ||||| || ||||| || |||||| |||||||||||||||| || || |||||||||||||| || ||||| ||||| ||| |||||||||| || |
--tttagaagcagttgtgtgatcccatttaagacccggaagaagaattcttagtaaaatgttaatgtggcttgtgtt-----tacaagtgtaattttgaatgtcaagGTGTTGGCTATCGAGGACGTGTTCAAGCATAGGGTGACAAATGTGGTTTTCATGGGAATGGGTGAGCCGATGTTGAACCTAAAGTCAGTACTTGATGCTC
upper sequence: GLYMA02G41500.1 (Glycine max), 3'ss of exon 5
lower sequence: Vv13s0019g01070.t01 (Vitis vinifera), 3'ss of exon 5
ggctttggatcattatcattgtgt----ttaggattgtaaaaattctgaaacaagcttagctttgtttactgcaagacggataaaattcatcttatgtgaacagGTCTTGGCCATTGAGGAGGTCTTCAAGAATAGGGTGACAAATGTAGTGTTTATGGGAATGGGTGAACCAATGTTAAACCTGAAGGCAGTACTTGAAGCAC
|| || ||| ||| | || | ||| |||| ||| | ||| | || | | ||| | |||||| |||||||||||| || |||||| |||| ||| | |||||||||||||| ||||||||||||||||| ||||||||||| |||||||| |||| ||||||| |
-aacttctatgtttaagatttgacagcatcagtttcactaaagctctgtgtt--tctttattcaacttagtacattgtgttttctattt-tactatgtgcacagGTCTTGGCAATAGAGGAGATCTTTAAGCAAAGGGTGACAAATGTGGTGTTTATGGGAATGGGCGAACCAATGTTGAACCTGAAATCAGTTATTGAAGCTCMapped 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|24136120|gb|BU926630.1|BU926630EST: GAAAAGGGGGGTTTTCAAGGAATCTTCAGAGACATGAAATAGTTGAACAG GTCTTGGCCATTGAGGAGGTCTTCAAGAATAGGGTGACAAATGTAGTGTTT
genomic: GAAAAGGGGGGTTTTCAAGGAATCTTCAGAGACATGAAATAGTTGAACAGgtctgtgtca ... atgtgaacagGTCTTGGCCATTGAGGAGGTCTTCAAGAATAGGGTGACAAATGTAGTGTTT
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.aacaagcttagctttgtttactgcaagacggataaaattcatcttatgtgaacagGTCTTGGCCATTGAGGAGGTCTTCAAGAATAGGGTGACAAATGTAGTGTTTATGGGAATGGGTGAACCAATGTTAAACCTGAAGGCAGTACTTGAAGCAC
ataaaattcatcttat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
ggctttggatcattatcattgtgtttaggattgtaaaaattctgaaacaagcttagctttgtttactgcaagacggataaaattcatcttatgtgaacagGTCTTGGCCATTGAGGAGGTCTTCAAGAATAGGGTGACAAATGTAGTGTTTATGGGAATGGGTGAACCAATGTTAAACCTGAAGGCAGTACTTGAAGCAC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGC
-gctttgg
- - - - - - - - - - - - - - - - - - - - - -gaaacaag
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tgcaaga
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ggataaaa