Sequence
atgc intronic sequence ATGC exonic sequence...agagaattaatgttatccgcctttttttgttgttatgataaaatgtgattgtgggctgtatttcttattatctgctattgcctttggctggtaccttcagGAGAGTGATGTGAAGTGGGCTTCAAGATGGGATGCCTATTTGCTAATGAATGATGATCAAATCCACTGGTTCTCAATTGTTAACTCATTAATGATTGTTC
Basic information
species | Glycine max |
transcript | GLYMA04G06420.1 |
intron # | 6 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA04G06420.1 (Glycine max), 3'ss of exon 6
lower sequence: GRMZM2G046005_T02 (Zea mays), 3'ss of exon 5
-agagaattaatgttatccgcctttttttgttg-ttatgataaaatgtgattgtgggctgtatttcttattatctgctattgcctttggctggtaccttcagGAGAGTGATGTGAAGTGGGCTTCAAGATGGGATGCCTATTTGCTAATGAATGATGATCAAATCCACTGGTTCTCAATTGTTAACTCATTAATGATTGTTC
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tgaatctatcacatgaactgcgttgtcaagttacttaacatacattttaaaatttgagtttgttt--taatgttttctgatttgcttggtattgctctgcagGAGAGTGATATCAAGTGGGCTTCTCGCTGGGACACCTACTTGTTAATGATAGATGATCAAATTCACTGGTTTTCTATTGTGAACTCTCTCATGATCGTAC
upper sequence: GLYMA04G06420.1 (Glycine max), 3'ss of exon 6
lower sequence: GRMZM2G180575_T01 (Zea mays), 3'ss of exon 6
agagaattaatgttatccgcctttttttgttgttatgataaaatgtgattgtgggctgtatttcttattatctgctattgcctttggctggta----ccttcagGAGAGTGATGTGAAGTGGGCTTCAAGATGGGATGCCTATTTGCTAATGAATGATGATCAAATCCACTGGTTCTCAATTGTTAACTCATTAATGATTGTTC
|||| || || | || | |||| | || || || | | ||| | ||| || | | |||| ||||| || |||||||||||| | ||||||||||| | ||||| |||| ||| |||||| ||||||||||| |||||||| || ||||| ||||| | ||||| || |
--tgaatctatcacataaactgcgttgtcaagttacta-aacatacatttcaaaatttgagttcgttttaa-tgttttctgatttgcttggtattgctctgcagGAGAGTGATATCAAGTGGGCTTCTCGCTGGGACACCTACTTGTTAATGATAGATGATCAAATTCACTGGTTTTCTATTGTGAACTCTCTCATGATCGTAC
upper sequence: GLYMA04G06420.1 (Glycine max), 3'ss of exon 6
lower sequence: AT5G10840.1 (Arabidopsis thaliana), 3'ss of exon 6
-agagaattaatgttatccgcctttttttgttgttatgataaaatgtgattgtgggctgtatttcttattatctgctattgcctttggctggtaccttcagGAGAGTGATGTGAAGTGGGCTTCAAGATGGGATGCCTATTTGCTAATGAATGATGATCAAATCCACTGGTTCTCAATTGTTAACTCATTAATGATTGTTC
|| || | | || || ||| | | ||||| | || ||| || || | | | ||| ||| | | | ||||| ||||| ||||||||||| || ||||||||| | ||| | || |||| |||| | ||||||||||||||||| || || || || | ||||| || |
gcaagttttttcttaagtaatctgcggtttgtgtcttaaaaaaatttcatgaattcttgttttcaatagtttttctgatttcctcttctgtttctgtccagGAAAGTGAAGTGAAGTGGGCATCTAGATGGGATACTTATCTTCTGATGAGTGATAACCAAATCCACTGGTTCTCTATCGTCAATTCTCTGATGATCGTCC
upper sequence: GLYMA04G06420.1 (Glycine max), 3'ss of exon 6
lower sequence: AT5G25100.1 (Arabidopsis thaliana), 3'ss of exon 6
----------agagaattaat--gttatccgcctttttttgttgttatgataaaatgtgattgtgggctgtatttcttattatctgctattgcctttggctggtaccttcagGAGAGTGATGTGAAGTGGGCTTCAAGATGGGATGCCTATTTGCTAATGAATGATGATCAAATCCACTGGTTCTCAATTGTTAACTCATTAATGATTGTTC
| |||| ||| | || | | |||| | | | || |||||| | |||| | | | | ||| || |||| | |||||||| ||||| ||||||||||| || ||||||||||| ||| | | |||| || ||||||| |||||||| || ||||| ||||| | ||||| || |
gcaagttcttgtttgactaatcagtttatcaccagatagttttgtcttagtgagatactattgtg--ttcctgttctcactgttt-tgatt--tttgcgctgatgtcttcagGAAAGTGAAGTGAAGTGGGCGTCTAGATGGGATGCTTATCTTTTGATGAGCGACAATCAAATTCACTGGTTTTCTATTGTCAACTCTCTTATGATCGTCC
upper sequence: GLYMA04G06420.1 (Glycine max), 3'ss of exon 6
lower sequence: Vv04s0008g06640.t01 (Vitis vinifera), 3'ss of exon 6
-----------agagaattaatgttatccgcctttttttgttgttatgataaaatgtgattgtgggctgtatttcttattatctgctattgcctttggctggtaccttcagGAGAGTGATGTGAAGTGGGCTTCAAGATGGGATGCCTATTTGCTAATGAATGATGATCAAATCCACTGGTTCTCAATTGTTAACTCATTAATGATTGTTC
| |||| || | | || |||||| | || || ||| || ||||||| | | | || | | ||| | | ||||| ||||||||||||||||| || ||||||||| ||||| | || |||| |||||| || ||||||||||||||||||||||| || || ||||||||||
ttaaccaagtttaataattggtgaaaagccaacttgcttgttgcccctgttaag-gttattatga-------ttcttatggttt-ttttttctcatctctgcca--tacagGAAAGTGATGTGAAGTGGGCATCTAGATGGGATACCTATCTTCTCATGAGTGATGACCAGATCCACTGGTTCTCAATTGTTAATTCTTTGATGATTGTTCMapped 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|193575245|gb|FK529362.1|FK529362EST: AGGTTGAAGAGGGCAAGGAAATTATCTTCACATATGATGTTGAATTCCAG GAGAGTGATGTGAAGTGGGCTTCAAGATGGGATGCCTATTTGCTAATGAAT
genomic: AGGTTGAAGAGGGCAAGGAAATTATCTTCACATATGATGTTGAATTCCAGgtgagtttat ... gtaccttcagGAGAGTGATGTGAAGTGGGCTTCAAGATGGGATGCCTATTTGCTAATGAAT
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tgattgtgggctgtatttcttattatctgctattgcctttggctggtaccttcagGAGAGTGATGTGAAGTGGGCTTCAAGATGGGATGCCTATTTGCTAATGAATGATGATCAAATCCACTGGTTCTCAATTGTTAACTCATTAATGATTGTTC
taccttc CT-rich tract
tgtatttcttattat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
agagaattaatgttatccgcctttttttgttgttatgataaaatgtgattgtgggctgtatttcttattatctgctattgcctttggctggtaccttcagGAGAGTGATGTGAAGTGGGCTTCAAGATGGGATGCCTATTTGCTAATGAATGATGATCAAATCCACTGGTTCTCAATTGTTAACTCATTAATGATTGTTC
- - - - - - - -tccgcct
- - - - - - - - - - - - - - - tgttatg
- - - - - - - - - - - - - - - - - - - - - - - - ttgtggg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tattgcc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ttggctg