Sequence
atgc intronic sequence ATGC exonic sequence...ttatcagcgccatatatatgtgtgtgtataccggtgcagaaaataccactttttccaaattttggtatgtttgatgctaaatatttgtctttattaatcaGGAGCTCATGTTGGAGGCCTACACAAGCAGCTGTGAAGTCCAATTTCCATCTCCCAATGCGCAGTTTTGAGTTAAAAAATA
Basic information
species | Glycine max |
transcript | GLYMA18G45380.1 |
intron # | 1 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA18G45380.1 (Glycine max), 3'ss of exon 1
lower sequence: AT2G45440.1 (Arabidopsis thaliana), 3'ss of exon 1
ttatcagcgccatatatatgtgtgtgtataccggtgcagaaaataccactttttccaaattttggtatgtttgatgctaaatatttgtct-ttattaatc----aGGAGCTCATGTTGGAGGCCTACACAAGCAGCTGTGAAGTCCAATTTCCATCTCCCAATGCGCAGTTTTGAGTTAAAAAATA-
|| |||||| | | | || | | ||||| | | ||| | || || || ||| | || |||| |||||||| ||| || | |||||||||| ||||||||||||||||||||||||| || ||| | ||||| |
--gtcta-atcatatagaaagacttcagttttataaataaagttgctttttttttcttacattgagacgtatggactcaagctcatgtgtgttgttaacacagAAGGAGCTCGAAATGGGTCTCTCCCAAAGCAGCTGTTGTACCCAATTTCCATCTCCCAATGCGCAGCTTGGAGGTTAAAAACAG
upper sequence: GLYMA18G45380.1 (Glycine max), 3'ss of exon 1
lower sequence: Vv15s0048g00750.t01 (Vitis vinifera), 3'ss of exon 1
--ttatcagcgccatatatat-gtgtgtgtataccggtgcagaaaataccactttttccaaattttggtatgtttgatgctaaatatttgtctttattaatcaGGAGCTCATGTTGGAGGCCTACACAAGCAGCTGTGAAGTCCAATTTCCATCTCCCAATGCGCAGTTTTGAGTTAAAAAATA-
| | | ||| |||| | || ||| | | | | | | | || || || | | |||| | || | |||| | || |||| | || ||||||||||||| | | |||||||||||||||||||| |||||||| | |||||||
gctaaatgccaccaattataaagcagatgaatat-gatctgtattgctgccatcatcctgggttgctatactaatgtattctattctttgccactaagcagGAGGAACGCAAAATGGAAGTCTGCACAAGCAGCTGTAATTCCTAATTTCCATCTCCCAATGCGTAGTTTTGAAGTTAAAAATAGMapped 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|151408385|gb|EV278193.1|EV278193EST: ATCCACCTTTCCCGTTTGCCCCTCCAATTTCACGAACACTAGAAACACCA GGAGCTCATGTTGGAGGCCTACACAAGCAGCTGTGAAGTCCAATTTCCATC
genomic: ATCCACCTTTCCCGTTTGCCCCTCCAATTTCACGAACACTAGAAACACCAggtccattct ... ttattaatcaGGAGCTCATGTTGGAGGCCTACACAAGCAGCTGTGAAGTCCAATTTCCATC
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ccactttttccaaattttggtatgtttgatgctaaatatttgtctttattaatcaGGAGCTCATGTTGGAGGCCTACACAAGCAGCTGTGAAGTCCAATTTCCATCTCCCAATGCGCAGTTTTGAGTTAAAAAATA
tgctaaa putative branch site (score: 2)
tttgtcttt putative PPT
taaatatttgtcttta 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
ttatcagcgccatatatatgtgtgtgtataccggtgcagaaaataccactttttccaaattttggtatgtttgatgctaaatatttgtctttattaatcaGGAGCTCATGTTGGAGGCCTACACAAGCAGCTGTGAAGTCCAATTTCCATCTCCCAATGCGCAGTTTTGAGTTAAAAAATA
- - - -cgccata
- - - - - - - - - -gtgtgtg
- - - - - - - - - - - - - - - ccggtgc
- - - - - - - - - - - - - - - - - - -agaaaata
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ggtatgt
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tgatgct