Sequence
atgc intronic sequence ATGC exonic sequence...gaaaagccttaaaagttgagcttaggttaattggttttaagggttccttttaagtcaagccctttaatgattgtgagtttctgtttgttggttgtgtcagCTTGTTTTTTAAACAGGAGATGGAACTTTCACTTGTTGGCCTTCAGAATGCTGGCAAGACTTCTCTTGTCAATGCAATTGCT
Basic information
species | Glycine max |
transcript | GLYMA02G41170.1 |
intron # | 1 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA02G41170.1 (Glycine max), 3'ss of exon 1
lower sequence: LOC_Os02g49980.2 (Oryza sativa), 3'ss of exon 1
gaaaagccttaaaagttgagcttaggttaattggttttaag---ggttccttttaagtcaagccctttaatgattgtgagtttctgtttgttggttgtgtcagCTTGTTTTTTAAACAGGAGATGGAACTTTCACTTGTTGGCCTTCAGAATGCTGGCAAGACTTCTCTTGTCAATGCAATTGCT
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---aaatattagaacatacgccaatattaagtactatgcaacatgtttccttataaacatgtctagtgaaaggtttactcatgacaattatgtcctccaccagCTTGTTTTTCAAGCAGGAGATGGAGCTCTCCCTGGTTGGCCTGCAGAATGCTGGGAAAACATCACTAGTTAATGCTGTTGCT
upper sequence: GLYMA02G41170.1 (Glycine max), 3'ss of exon 1
lower sequence: GRMZM2G089454_T01 (Zea mays), 3'ss of exon 1
-----gaaaagccttaaaagttgagcttaggttaattggttttaag-ggttccttttaagtca-agccctttaatgattgtgagtttctgtttgttggttgtgtcagCTTGTTTTTTAAACAGGAGATGGAACTTTCACTTGTTGGCCTTCAGAATGCTGGCAAGACTTCTCTTGTCAATGCAATTGCT
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gaaattagcatctgtaccagt-gtgtacattttgatggcttttaagcagtgcatattgatttgtagcaattctactcatggcagtaa-tattt-----ctatttcagCTTGTTTTTTAAGCAAGAAATGGAACTCTCCCTGGTTGGGTTGCAGAATGCTGGGAAGACATCGCTGGTCAATGCTGTTGCT
upper sequence: GLYMA02G41170.1 (Glycine max), 3'ss of exon 1
lower sequence: GRMZM2G089454_T04 (Zea mays), 3'ss of exon 1
gaaaagccttaaaagttgagcttaggttaattggttttaagggttccttttaagtcaagccctttaatgattgtgagtttctgtttgttggttgtgtcagCTTGTTTTTTAAACAGGAGATGGAACTTTCACTTGTTGGCCTTCAGAATGCTGGCAAGACTTCTCTTGTCAATGCAATTGCT----------------------------------------------------------------
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-----------------------------------agtgcatattgatttgtag-caattctactcatggcagtaa-----tattt-----ctatttcagcttgttttttaagcaagaaatggaactctccctggttgggttgcagAATGCTGGGAAGACATCGCTGGTCAATGCTGTTGCTGTATGCATCAACTCAGTCAAGATACATTACCATGTTATCTGGTGTTTTGATTTTAATTCATGGC
upper sequence: GLYMA02G41170.1 (Glycine max), 3'ss of exon 1
lower sequence: AT5G37680.1 (Arabidopsis thaliana), 3'ss of exon 1
gaaaagccttaaaagttgagcttaggttaattggtttta--agggttccttttaagtcaagccctt-taatgattgtgagtttctgtttgttggttgtgtcagCTTGTTTTTTAAACAGGAGATGGAACTTTCACTTGTTGGCCTTCAGAATGCTGGCAAGACTTCTCTTGTCAATGCAATTGCT
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---tgttgtttttggttatacttatgtttttagtgtatagcagaatcacgttttggtaacacttagattttgattctgtgtttgcttatatttgttgtgtcagCTTGTTTTTCAAACAAGAGATGGAGCTGTCACTCGTTGGACTTCAAAATGCTGGGAAGACTTCTCTTGTCAATGCCATTGCT
upper sequence: GLYMA02G41170.1 (Glycine max), 3'ss of exon 1
lower sequence: Vv14s0006g01090.t01 (Vitis vinifera), 3'ss of exon 2
gaaaagccttaaaagttgagcttaggttaattggttttaagggttccttttaagtcaagccctttaatgattgtgagtttctgtttgttggttgtgtcagCTTGTTTTTTAAACAGGAGATGGAACTTTCACTTGTTGGCCTTCAGAATGCTGGCAAGACTTCTCTTGTCAATGCAATTGCT
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-------gttagtatcatatttttcataacagaatattgatttctccttatttatgaagtcctcct-cgcttac-----cttgtct-----ccatatcagCTTATTTTATAAACAGGAAATGGAACTTTCTCTTATAGGCCTTCAGAATGCAGGAAAGACATCTCTTCTTAATGCCATTGCTMapped 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|151393791|gb|EV263666.1|EV263666EST: GATTCACACACAATGGGTCTCTGGGATTCCTTCCTCAATTGGCTCCGCAG CTTGTTTTTTAAACAGGAGATGGAACTTTCACTTGTTGGCCTTCAGAATGC
genomic: GATTCACACACAATGGGTCTCTGGGATTCCTTCCTCAATTGGCTCCGCAGgtaaacctct ... gttgtgtcagCTTGTTTTTTAAACAGGAGATGGAACTTTCACTTGTTGGCCTTCAGAATGC
EST:
gi|8826727|gb|BE210457.1|BE210457EST: GATTCACACACAATGGGTCTCTGGGATTCCTTCCTCAATTGGCTCCGCAG CTTGTTTTTTAAACAGGAGATGGAACTTTCACTTGTTGGCCTTCAGAATGC
genomic: GATTCACACACAATGGGTCTCTGGGATTCCTTCCTCAATTGGCTCCGCAGgtaaacctct ... gttgtgtcagCTTGTTTTTTAAACAGGAGATGGAACTTTCACTTGTTGGCCTTCAGAATGC
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ccttttaagtcaagccctttaatgattgtgagtttctgtttgttggttgtgtcagCTTGTTTTTTAAACAGGAGATGGAACTTTCACTTGTTGGCCTTCAGAATGCTGGCAAGACTTCTCTTGTCAATGCAATTGCT
ctttaat putative branch site (score: 4)
tttaatgatt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gaaaagccttaaaagttgagcttaggttaattggttttaagggttccttttaagtcaagccctttaatgattgtgagtttctgtttgttggttgtgtcagCTTGTTTTTTAAACAGGAGATGGAACTTTCACTTGTTGGCCTTCAGAATGCTGGCAAGACTTCTCTTGTCAATGCAATTGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ATGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAGA
gaaaagc
- - - - - - - - - - - - - - - - - - - - - - - - - - - -caagccc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - gattgtg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - gtttctg