Sequence
atgc intronic sequence ATGC exonic sequence...taagcatgcatgaagtttggttccatgtcttgatataccaaaacaaatgacaaaaaatgatcctgaaagctcaaactgactgtactttggtatcttatagAGGTGCCAGAGCAGCAGTGTGGGAGAACTTTAAGGACAATCCACTGTTTGACATTTCCACTGAGCATCCAACAACATATTACGAGGATATGCAACGAGCA
Basic information
species | Glycine max |
transcript | GLYMA04G37920.1 |
intron # | 3 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA04G37920.1 (Glycine max), 3'ss of exon 3
lower sequence: LOC_Os01g70190.1 (Oryza sativa), 3'ss of exon 3
-taagcatgcatgaagtttggt---tccatgtcttgatatac-caaaacaaatgacaaaaaatgatcctgaaagctcaaactgactgtactttggtatcttatagAGGTGCCAGAGCAGCAGTGTGGGAGAACTTTAAGGACAATCCACTGTTTGACATTTCCACTGAGCATCCAACAACATATTACGAGGATATGCAACGAGCA
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gtgagcaccaagaacatgcaatcactcgatgcttcctcataagcattgttgatgaattattgtaacccaaaagtcttga--tgaacctgcttta-tgcaatgcagAGGTGCCCGTGCATCGGTGTGGGAGAACTTCAAGAACAATCCTCTTTTTGACATCTCCACAGACCACCCACCAACCTACTACGAGGACATGCAGCGTTCC
upper sequence: GLYMA04G37920.1 (Glycine max), 3'ss of exon 3
lower sequence: AT5G61840.1 (Arabidopsis thaliana), 3'ss of exon 3
-------------------------------------------------------------------------------taagcatgcatgaagtttggttccatgtcttgatataccaaaacaaatga---------------caaaaaatgatcctgaaagc--tcaaactgactgtactttggtatcttatagAGGTGCCAGAGCAGCAGTGTGGGAGAACTTTAAGGACAATCCACTGTTTGACATTTCCACTGAGCATCCAACAACATATTACGAGGATATGCAACGAGCA
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gtaatttttttcttatgaaagttcttagctattgttcataataaatttcataaatctcctaaaacagttcataattgctttatcggtttggaattttggacataaaactcaaaaaaggaaaatttatcagactgtttttagagccatggattgttcttataatcagtgatgatgtttgtttgtcaaactggcacagGGGTGCAAGAGCAGCTGTATGGGAAAACTTCAAAGACAATCCGCTGTTTGACATCTCAACAGAGCACCCAACAACATATTATGAGGACATGCAGAGAGCA
upper sequence: GLYMA04G37920.1 (Glycine max), 3'ss of exon 3
lower sequence: Vv17s0000g00120.t01 (Vitis vinifera), 3'ss of exon 3
-----taagcatgcatgaagtttggttccatgtcttgatataccaaaacaaatgacaaaaaatgatcctgaaagctcaaactgactgtactttggta--tcttatagAGGTGCCAGAGCAGCAGTGTGGGAGAACTTTAAGGACAATCCACTGTTTGACATTTCCACTGAGCATCCAACAACATATTACGAGGATATGCAACGAGCA
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attgttttttgttccttaa--tttgtccaatgatctttaatat-gaaatttatgccaag--atgttttttaa--tccaactttttttttttttggacatttttgcagAGGCGCACGGGCAGCTGTGTGGGAGAATTTTAAAGACAATCCACTTTTTGACATCTCAACAGAGCACCCAATGACTTATTATGAGGACATGCAACGGGCT
upper sequence: GLYMA04G37920.1 (Glycine max), 3'ss of exon 3
lower sequence: Vv01s0150g00180.t01 (Vitis vinifera), 3'ss of exon 3
--taagcatgcatgaagtttggttccatgtcttgatataccaaaacaaatgacaaaaaatgatcctgaaagctcaaactgactgtactttggtatcttatagAGGTGCCAGAGCAGCAGTGTGGGAGAACTTTAAGGACAATCCACTGTTTGACATTTCCACTGAGCATCCAACAACATATTACGAGGATATGCAACGAGCA
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aggaagca-acatcttgtatgatac-atggctttgtcttttatattaggtcctttgggttgaatgaatcaactcctatctaactcttttaattgattgacagAGGTGCAAGGGCAGCAGTTTGGGAGAACTTTAAGGACAACCCGCTCTTTGACATCTCCACTGAGCACCCAACGACATATTATGAAGACATGCAACGTGCTMapped 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|151411015|gb|EV280826.1|EV280826EST: GGACTGTTTTATGATGTTGGAAATGACCCTGAAGGTGGATACTATGCAAG AGGTGCCAGAGCAGCAGTGTGGGAGAACTTTAAGGGCAATCCACTGTTTGA
genomic: GGACTGTTTTATGATGTTGGAAATGACCCTGAAGGTGGATACTATGCAAGgtatgtctta ... tatcttatagAGGTGCCAGAGCAGCAGTGTGGGAGAACTTTAAGGACAATCCACTGTTTGA
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.aatgacaaaaaatgatcctgaaagctcaaactgactgtactttggtatcttatagAGGTGCCAGAGCAGCAGTGTGGGAGAACTTTAAGGACAATCCACTGTTTGACATTTCCACTGAGCATCCAACAACATATTACGAGGATATGCAACGAGCA
aactgac putative branch site (score: 2)
aaaaaatgat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
taagcatgcatgaagtttggttccatgtcttgatataccaaaacaaatgacaaaaaatgatcctgaaagctcaaactgactgtactttggtatcttatagAGGTGCCAGAGCAGCAGTGTGGGAGAACTTTAAGGACAATCCACTGTTTGACATTTCCACTGAGCATCCAACAACATATTACGAGGATATGCAACGAGCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGGAT
- -gcatgca
- - - - - - - - - - - -catgtct
- - - - - - - - - - - - - - - - - - -ccaaaac
- - - - - - - - - - - - - - - - - - - - - - - - - -aaaaaat
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tcctgaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ctcaaac
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - actgtac