Sequence
atgc intronic sequence ATGC exonic sequencegttgggaattgatttggcatatggtagttcaattatgtttgtacacaaattagaatgatgtgtgcttgcatgcagGTTGAATTTAACAAGGCTGCACAGTCTTTGACGGAGGCTACAATTCCAACCACTCAGAAGAAAACTGCCTTGAATCGGCTGGTTAAG
Basic information
species | Glycine max |
transcript | GLYMA09G15980.2 |
intron # | 4 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA09G15980.2 (Glycine max), 3'ss of exon 4
lower sequence: AT3G58560.1 (Arabidopsis thaliana), 3'ss of exon 4
gttgggaattgatttggcatatggtagttcaattatgtttgtacacaaattagaatgatgtgtgcttgcatgcagGTTGAATTTAACAAGGCTGCACAGTCTTTGACGGAGGCTACAATTCCAACCACTCAGAAGAAAACTGCCTTGAATCGGCTGGTTAAG
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-gtatgtcttagttt--tctcctgttacctatctaattaggcccatttgctaaatcattgggctgct-catccagGTTGAGTTCAACAAGGCTGCACAGTCTTTGACTGAGGCTATTATCCCTGTTTCCCAGAAGAAAAATGCTTTGAATCGGTTGGTCAAG
upper sequence: GLYMA09G15980.2 (Glycine max), 3'ss of exon 4
lower sequence: AT3G58580.1 (Arabidopsis thaliana), 3'ss of exon 4
gttgggaattgatttggcatatggtagttcaattatgtttgtacacaaattagaatgatgtgtg---cttgcatgcagGTTGAATTTAACAAGGCTGCACAGTCTTTGACGGAGGCTACAATTCCAACCACTCAGAAGAAAACTGCCTTGAATCGGCTGGTTAAG
||| | | | || ||||| | | | ||| || | | || || | || ||||||||||| ||||||||||| ||||||||||| || ||| ||| || ||||||||| |||||| || || || |||||||||
gtttgtattcagttc--tatatgtttacttgctagatccagtaagatctctatactaattcatggactgtaaatccagGTTGAATTCAACAAGGCTGCTCAGTCTTTGACTGACGCTCTAATCCCTCAGGCTCAGAAGAGAACTGCTTTAAACCGACTGGTTAAG
upper sequence: GLYMA09G15980.2 (Glycine max), 3'ss of exon 4
lower sequence: Vv08s0007g07020.t01 (Vitis vinifera), 3'ss of exon 4
gttgggaattgatttggcatatgg----tagttcaattatgtttgtacacaaattagaat-gatgtgtgcttgcatgcagGTTGAATTTAACAAGGCTGCACAGTCTTTGACGGAGGCTACAATTCCAACCACTCAGAAGAAAACTGCCTTGAATCGGCTGGTTAAG
|| ||| || |||| ||||| |||| | ||| | ||| || ||| ||| | |||||| || |||||||||||||| |||||||| |||||||||||||| ||| |||||| |||| ||||||||||| | ||||| || ||||||
gtaatgaagtg-tttgtattatggactccagttttctgtggttattgcacttgctaaaatagatttatgcttgtatacagGTTGAATTTAATAAGGCTGCCCAGTCTTTGACGGACGCTGTGGTTCCAAGTGCTCAAAAGAAAACTGCTCTAAATCGACTAGTTAAGMapped 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|18848623|gb|BM567768.1|BM567768EST: GTGCAACATTTTTCCGTAGAGACAGATTTTCACATGTTAAGAAATACGAG GTTGAATTTAACAAGGCTGCACAGTCTTTGACGGAGGCTACAATTCCAACC
genomic: GTGCAACATTTTTCCGTAGAGACAGATTTTCACATGTTAAGAAATACGAGgttgggaatt ... ttgcatgcagGTTGAATTTAACAAGGCTGCACAGTCTTTGACGGAGGCTACAATTCCAACC
EST:
gi|27426055|gb|CA937575.1|CA937575EST: GTGCAACATTTTTCCGTAGAGACAGATTTTCACATGTTAAGAAATACGAG GTTGAATTTAACAAGGCTGCACAGTCTTTGACGGAGGCTACAATTCCAACC
genomic: GTGCAACATTTTTCCGTAGAGACAGATTTTCACATGTTAAGAAATACGAGgttgggaatt ... ttgcatgcagGTTGAATTTAACAAGGCTGCACAGTCTTTGACGGAGGCTACAATTCCAACC
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.atggtagttcaattatgtttgtacacaaattagaatgatgtgtgcttgcatgcagGTTGAATTTAACAAGGCTGCACAGTCTTTGACGGAGGCTACAATTCCAACCACTCAGAAGAAAACTGCCTTGAATCGGCTGGTTAAG
aattatgttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gttgggaattgatttggcatatggtagttcaattatgtttgtacacaaattagaatgatgtgtgcttgcatgcagGTTGAATTTAACAAGGCTGCACAGTCTTTGACGGAGGCTACAATTCCAACCACTCAGAAGAAAACTGCCTTGAATCGGCTGGTTAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAA