Sequence
atgc intronic sequence ATGC exonic sequence...ccagtaattcagattgtgtttatgacctactcattggtcgattctctctatctagtgaatttcgagaaattatctaacagttaaagtaaaacctttacagACAATAAAGACAAATGTGATTGGAACACTGAACATGCTTGGGCTTGCTAAGCGTGTGGGAGCAAG
Basic information
species | Glycine max |
transcript | GLYMA11G15010.1 |
intron # | 5 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA11G15010.1 (Glycine max), 3'ss of exon 5
lower sequence: AT5G59290.2 (Arabidopsis thaliana), 3'ss of exon 4
ccagtaattcagattgtgtttatgacctactcattggtcgattctctctatctagtgaatttcgagaaattatctaacagttaaagtaaaacctttacagACAATAAAGACAAATGTGATTGGAACACTGAACATGCTTGGGCTTGCTAAGCGTGTGGGAGCAAG
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-----------gttcgtgtgaat-atagatatattctcatatcaccttcatataatcagaatcg-----ttagttactgatctaa--tatgtttatgcagACAATCAAGACCAATGTGATTGGTACACTCAACATGCTCGGTCTTGCCAAGCGTGTTGGAGCAAG
upper sequence: GLYMA11G15010.1 (Glycine max), 3'ss of exon 5
lower sequence: AT2G28760.1 (Arabidopsis thaliana), 3'ss of exon 4
ccagtaattcagattgtgtttat---gacctactcattggtcgattctctctatctagtgaatttcgagaaattatctaacagttaaagtaaaacctttacagACAATAAAGACAAATGTGATTGGAACACTGAACATGCTTGGGCTTGCTAAGCGTGTGGGAGCAAG-----------------------------------
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---gtttgttaaacttcgttaatcaaaactcgcaaaatgctagctgatatattttta-tgacttatga----tcatatatccttttcatctttctaatggcagACGATAAAAACAAATGTGATTGGCACACTTAACATGTTAGGACTAGCTAAGCGAGTTGGAGCAAGAATTTTACTTACTTCCACATCTGAAGTGTATGGTG
upper sequence: GLYMA11G15010.1 (Glycine max), 3'ss of exon 5
lower sequence: Vv06s0004g04390.t01 (Vitis vinifera), 3'ss of exon 5
ccagtaattcagattgtgtttatgacctactcattggtcgattctctctatctagtgaatttcgagaaattatctaacagttaaagtaaa-----acctttacagACAATAAAGACAAATGTGATTGGAACACTGAACATGCTTGGGCTTGCTAAGCGTGTGGGAGCAAG
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-ttgacgtctagatttt--ttgtgttcaat--gtcagtgcagtcatttgaacttgtgaattattgagaattgtctgacttttttacttaactgtcactttaacagACAATAAAAACAAACGTCATTGGTACACTGAATATGCTGGGACTTGCCAAACGAGTTGGAGCAAG
upper sequence: GLYMA11G15010.1 (Glycine max), 3'ss of exon 5
lower sequence: PP1S189_118V6.1 (Physcomitrella patens), 3'ss of exon 5
ccagta-attcagattgtgtttatgacctactcattggtcgattctctctatctagtgaatttcgagaaattatctaacagttaaagtaaaacct----ttacagACAATAAAGACAAATGTGATTGGAACACTGAACATGCTTGGGCTTGCTAAGCGTGTGGGAGCAAG
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----tatatatatataagaatccttgagcgtttgtagagtgaagagatatgtgcgtttcagtttcagat-tggtttgaaatttggtttgaaacttcattttgcagACCATCAAGACAAATGTGATTGGTACGCTCAACATGCTTGGACTCGCTAAACGAGTTGGTGCAAGMapped 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|22525432|gb|BU084243.1|BU084243EST: ATCTTGCATGCTCTGCTTCTCCAATCTTCTACAAATACAACCCTGTAAAG ACAATAAAGACAAATGTGATTGGAACACTGAACATGCTTGGGCTTGCTAAG
genomic: ATCTTGCATGCCCTGCTTCTCCAATCTTCTACAAATACAACCCTGTAAAGgtgggggttc ... acctttacagACAATAAAGACAAATGTGATTGGAACACTGAACATGCTTGGGCTTGCTAAG
EST:
gi|18040716|gb|BM309010.1|BM309010EST: ATCTTGCATGCCCTGCTTCTCCAATCTTCTACAAATACAACCCTGTAAAG ACAATAAAGACAAATGTGATTGGAACACTGAACATGCTTGGGCTTGCTAAG
genomic: ATCTTGCATGCCCTGCTTCTCCAATCTTCTACAAATACAACCCTGTAAAGgtgggggttc ... acctttacagACAATAAAGACAAATGTGATTGGAACACTGAACATGCTTGGGCTTGCTAAG
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ctctatctagtgaatttcgagaaattatctaacagttaaagtaaaacctttacagACAATAAAGACAAATGTGATTGGAACACTGAACATGCTTGGGCTTGCTAAGCGTGTGGGAGCAAG
atctaac putative branch site (score: 2)
cctttac putative PPT
aaattatctaa 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
ccagtaattcagattgtgtttatgacctactcattggtcgattctctctatctagtgaatttcgagaaattatctaacagttaaagtaaaacctttacagACAATAAAGACAAATGTGATTGGAACACTGAACATGCTTGGGCTTGCTAAGCGTGTGGGAGCAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCAAG
- - - - - -gattgtg
- - - - - - - - - - - - - ctactca