Sequence
atgc intronic sequence ATGC exonic sequence...ttatagttgtaaaatttatgttattctatttaatctttcacactttgatagttctacttcttaccttgaatctgatctgacctgtcctctgcaattgcagGGGGGAAGCGTCTTGTGCCAGTGGGCCTAGGAGATGATGATCAATGCATTGAGGATGACTTTACTGCATG
Basic information
species | Glycine max |
transcript | GLYMA13G00990.1 |
intron # | 6 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA13G00990.1 (Glycine max), 3'ss of exon 6
lower sequence: LOC_Os08g14570.1 (Oryza sativa), 3'ss of exon 5
ttatagttgtaaaatttatgttattctatttaatctttcacactttgatagttctacttcttaccttgaatctgatctgacctgtcctctgcaattgcagGGGGGAAGCGTCTTGTGCCAGTGGGCCTAGGAGATGATGATCAATGCATTGAGGATGACTTTACTGCATG
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--------------------gtgtgcctcatgactgccctgccctacagacttttgatatatctgttcagttt-atctcaagcattttgtgtttgtttagGTGGAAAACGTCTTGTTCCGGTTGGTCTTGGAGATGATGATCAATGCATTGAGGATGACTTCAACGCATG
upper sequence: GLYMA13G00990.1 (Glycine max), 3'ss of exon 6
lower sequence: GRMZM2G144407_T01 (Zea mays), 3'ss of exon 6
ttatagttgtaaaatttatgttattctatttaatctttcacactttgatagttctacttcttaccttgaatctgatctgacc---tgtcctctgcaattgcagGGGGGAAGCGTCTTGTGCCAGTGGGCCTAGGAGATGATGATCAATGCATTGAGGATGACTTTACTGCATG
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---------------gtatgcaccccccttgagtctttagtatcctctcagg-ctacct-ttatgttcag-ctgatcttattaagtattaaatgtttttgtagGCGGAAAGCGCCTTGTTCCAGTTGGTCTTGGAGATGATGACAAATGCATTGAGGATGACTTCAACACATG
upper sequence: GLYMA13G00990.1 (Glycine max), 3'ss of exon 6
lower sequence: AC217947.4_FGT002 (Zea mays), 3'ss of exon 5
ttatagttgtaaaatttatgttattctatttaatctttcacactttgatagttctacttcttaccttgaatctgatctgacctgtcctctgcaattgcagGGGGGAAGCGTCTTGTGCCAGTGGGCCTAGGAGATGATGATCAATGCATTGAGGATGACTTTACTGCATG
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--------gtatgcccctttgagtcttcagtatcctatcacgctgtcttttttctagttaatatgttcaa-ctgatcttaagtattttatgtttgcttagGTGGAAAGCGCCTTGTTCCAGTTGGTCTTGGGGACGATGACCAATGCATTGAGGATGACTTCAATGCATG
upper sequence: GLYMA13G00990.1 (Glycine max), 3'ss of exon 6
lower sequence: Vv11s0052g00880.t01 (Vitis vinifera), 3'ss of exon 6
ttatagttgtaaaatttatgttattctatttaatctttcacactttgatagttctacttcttaccttgaatc--tgatctgacctgtcctctgca-attgcagGGGGGAAGCGTCTTGTGCCAGTGGGCCTAGGAGATGATGATCAATGCATTGAGGATGACTTTACTGCATG
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--agagatgaaaagatt-tattgctataattagcttgttgagttgtgcttctattttcatcaaattcgttcccttgagctgacatgatctttattcatttcagGTGGAAAGCGCATTGTCCCAGTGGGTCTTGGGGATGATGACCAATGCATTGAGGATGACTTCGCTGCATGMapped 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|208071033|gb|GD871794.1|GD871794EST: GTGGCGAAGGTAGTGGATGACATGCTTGCTGAGCAAG GGGGGAAGCGTCTTGTGCCA
genomic: GTGGCGAAGGTAGTGGATGACATGCTTGCTGAGCAAGgtattctatt ... gcaattgcagGGGGGAAGCGTCTTGTGCCA
EST:
gi|209729001|gb|BW655031.1|BW655031EST: GTGGCGAAGGTAGTGGATGACATGCTTGCTGAGCAAG GGGGGAAGCGTCTTGTGCCAGTGGGCCTAGGAGATGATGATNCA-TGCATT
genomic: GTGGCGAAGGTAGTGGATGACATGCTTGCTGAGCAAGgtattctatt ... gcaattgcagGGGGGAAGCGTCTTGTGCCAGTGGGCCTAGGAGATGATGAT-CAATGCATT
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tgatagttctacttcttaccttgaatctgatctgacctgtcctctgcaattgcagGGGGGAAGCGTCTTGTGCCAGTGGGCCTAGGAGATGATGATCAATGCATTGAGGATGACTTTACTGCATG
tcctctgc CT-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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
ttatagttgtaaaatttatgttattctatttaatctttcacactttgatagttctacttcttaccttgaatctgatctgacctgtcctctgcaattgcagGGGGGAAGCGTCTTGTGCCAGTGGGCCTAGGAGATGATGATCAATGCATTGAGGATGACTTTACTGCATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGGATG
- - - - - - - - - - - - - - - - - - ttcacac
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ctgacct