Sequence
atgc intronic sequence ATGC exonic sequencegtgagttgtctttacaactaaatatgcagtttcaatcagcagatcaccatccatgtttatctgtgcataaaaaatggttacttgcagcattgaaatcgtatctgttattctacatctcagagttggttatttggcatcagaatgatccaatctgattggatggtggatatgttcctcagACGTTTGTTGGAACTCCATTCTGGATGGCTCCAGAGGTTATACAGAACTCTGGAGATGGCTACGATGAGAAG
Basic information
species | Physcomitrella patens |
transcript | PP1S98_82V6.2 |
intron # | 7 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: PP1S98_82V6.1 (Physcomitrella patens), 3'ss of exon 7
lower sequence: LOC_Os07g32400.2 (Oryza sativa), 3'ss of exon 7
gtgagttgtctttacaactaaatatgcagtttcaatcagcagatcaccatccatgtttatctgtgcataaaaaatggttacttgcagcattgaaatcgtatctgttat-tctacatctcagagttggttatttggcatcagaatgatccaatctgattggatggtggatatg--ttcctcagACGTTTGTTGGAACTCCATTCTGGATGGCTCCAGAGGTTATACAGAACTCTGGAGATGGCTACGATGAGAAG
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---------------------------------------------------------------------------------ctgttctgctagtatcat-tcggtagtgtttttagctcaaggacaaacctttgcttttggaaggtaatattgctaatggcttttaattttgaattgtgtagACATTTGTTGGAACTCCCTTTTGGATGGCACCTGAGGTTATTCAAAACTCTG---ACGGGTACAATGAAAAG
upper sequence: PP1S98_82V6.1 (Physcomitrella patens), 3'ss of exon 7
lower sequence: GRMZM2G027756_T02 (Zea mays), 3'ss of exon 4
gtgagttgtctttacaactaaatatgcagtttcaatcagcagatcaccatccatgtttatctgtgcataaaaaatggttacttgcagcattgaaatcgtatctgttattctacatctcagagttggttatttggcatcagaatgatccaatctgattggatggtggatatgttcctcagACGTTTGTTGGAACTCCATTCTGGATGGCTCCAGAGGTTATACAGAACTCTGGAGATGGCTACGATGAGAAG
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-------------------------------------------------------------------------tttaaattttatggcaa-aatattctctttgaaaaattacatt----gattaaagggtgagcatttgtactg-ctggtctgctgctaatgatttcaaactgttcagACATTTGTTGGAACTCCCTTTTGGATGGCACCTGAGGTTATTCAAAATTCTGAAG---GGTACAATGAGAAG
upper sequence: PP1S98_82V6.1 (Physcomitrella patens), 3'ss of exon 7
lower sequence: GLYMA13G34970.1 (Glycine max), 3'ss of exon 8
gtgagttgtctttacaactaaatatgcagtttcaatcagcagatcaccatccatgtttatctgtgcataaaaaatggttacttgcagcattgaaatcgta-tctgttattctacatctcagagttggttatttggcatcagaatgatccaatctgattggatggtggatatgttcctcagACGTTTGTTGGAACTCCATTCTGGATGGCTCCAGAGGTTATACAGAACTCTGGAGATGGCTACGATGAGAAG
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-------------------------------------------------------atactttgtgcaattaaaa-aatcacttggagttctaaattagtactctacagctcttcatctttga-ctggatacatatttt-------------tttttttatatcataa----------cagACATTTGTAGGAACACCATTCTGGATGGCACCTGAGGTTATTCAGAATACTG---ATGGATATAATGAGAAG
upper sequence: PP1S98_82V6.1 (Physcomitrella patens), 3'ss of exon 7
lower sequence: GLYMA12G35510.1 (Glycine max), 3'ss of exon 7
gtgagttgtctttacaactaaatatgcagtttcaatcagcagatcaccatccatgtttatctgtgcataaaaaatggttacttgcagcattgaaatcgtatctgttattctacatctcagagttggttatttggcatcagaatgatccaatctgattggatggtggatatgttcctcagACGTTTGTTGGAACTCCATTCTGGATGGCTCCAGAGGTTATACAGAACTCTGGAGATGGCTACGATGAGAAG
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---------------------------------------------------------------tgcatttaatac-----tttgtgcaattgaaaaatcacttagatttttaaatttttactcttcatctttgac-tggatatgctaacatttttttttatcataa----------cagACATTTGTAGGAACACCATTCTGGATGGCACCTGAGGTTATTCAGAATAC---AGATGGATATAATGAGAAG
upper sequence: PP1S98_82V6.1 (Physcomitrella patens), 3'ss of exon 7
lower sequence: Vv19s0014g02310.t01 (Vitis vinifera), 3'ss of exon 8
gtgagttgtctttacaactaaatatgcagtttcaatcagcagatcaccatccatgtttatctgtgcataaaaaatggttacttgcagcattgaaatcgtatctgtta-ttctacatctcaga-gttggttatttggcatcagaatgatccaatctgattggatggtggatatgttcctcagACGTTTGTTGGAACTCCATTCTGGATGGCTCCAGAGGTTATACAGAACTCTGGAGATGGCTACGATGAGAAG
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----------------------------------------------------------------------------gctag--gaaccaatgaa--catgtctaaaagttgaatggatcgaatgcctcttacttcatttcatgat-atatatttttacactaatgtgtttaacaatgacagACATTTGTAGGAACACCATTCTGGATGGCTCCAGAGGTAATTCAGAATTC---AGAAGGATATAATGAGAAGMapped 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|162256992|gb|FC432731.1|FC432731EST: CAGACTTTGGAGTTTCCGCCCAGCTGACACGGACTATGTCCAAACGCAAG ACGTTTGTTGGAACTCC
genomic: CAGACTTTGGAGTTTCCGCCCAGCTGACACGGACTATGTCCAAACGCAAGgtgagttgtc ... tgttcctcagACGTTTGTTGGAACTCC
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ggttatttggcatcagaatgatccaatctgattggatggtggatatgttcctcagACGTTTGTTGGAACTCCATTCTGGATGGCTCCAGAGGTTATACAGAACTCTGGAGATGGCTACGATGAGAAG
atctgat putative branch site (score: 4)
tgttcctc putative PPT
atatgtt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtgagttgtctttacaactaaatatgcagtttcaatcagcagatcaccatccatgtttatctgtgcataaaaaatggttacttgcagcattgaaatcgtatctgttattctacatctcagagttggttatttggcatcagaatgatccaatctgattggatggtggatatgttcctcagACGTTTGTTGGAACTCCATTCTGGATGGCTCCAGAGGTTATACAGAACTCTGGAGATGGCTACGATGAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGATG