Sequence
atgc intronic sequence ATGC exonic sequence...attggtatcctaaaaaatacagctagtctgttggttttataattcgtgtttttgtgatacgtgatgaaataaatatcggctctgatgggaagtggtgcagGTTGCAGATTTTGGAGTTTCTGCTCAGCTGACTCGTACAATGTCCAAACGCAAG
Basic information
species | Physcomitrella patens |
transcript | PP1S59_173V6.2 |
intron # | 4 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: PP1S59_173V6.1 (Physcomitrella patens), 3'ss of exon 5
lower sequence: GLYMA12G35510.1 (Glycine max), 3'ss of exon 6
---attggtatcctaaaaaa---tacagctagtctgttggttttataa---ttcgtgtttttgtgatac-----gtgat--gaaataaatatcggctctgatgggaagtggtgc-agGTTGCAGATTTTGGAGTTTCTGCTCAGCTGACTCGTACAATGTCCAAACGCAAG
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gtacgttatattctgacagaggttatatacaatttgtttattttatatgacttcattgaaaaatgatgcacctaataatttgagatgtggacttgcatacatgtggaatgtcaccagGTTGCAGATTTTGGTGTTTCTGCTCAATTAACAAGGACTATATCAAGGAGAAAG
upper sequence: PP1S59_173V6.1 (Physcomitrella patens), 3'ss of exon 5
lower sequence: GLYMA13G34970.1 (Glycine max), 3'ss of exon 7
--at-tggtatcctaaaaaat-acagctagtctgttggttttataatt-cgtgtttttgtgatacgtga-------tgaaataaatatcggctctgatgggaagtggtgc-agGTTGCAGATTTTGGAGTTTCTGCTCAGCTGACTCGTACAATGTCCAAACGCAAG
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gtatgttatattctgacaggttatatccaatttgtttattttatgatttcattgaaaaatgatgcatgtaataatttgagatacggacttgcatacatgtggaatgtcaccagGTTGCAGATTTTGGTGTTTCTGCTCAATTGACAAGGACTATATCAAGGAGAAAG
upper sequence: PP1S59_173V6.1 (Physcomitrella patens), 3'ss of exon 5
lower sequence: EFJ32910 (Selaginella moellendorffii), 3'ss of exon 6
attggtatcctaaaaaatacagctagtctgttggttttataatt-cgtgtttttgtgatacgtgatgaaataaatatcggctctgatgggaagtggtgcagGTTGCAGATTTTGGAGTTTCTGCTCAGCTGACTCGTACAATGTCCAAACGCAAG
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--------------------------------------gtaactgcgtggtttagaaggtcgtgattgtactcatatt-----ttataaaa-------cagGTTGCAGATTTTGGGGTTTCTGCTCAGCTCACACGTACTGTGTCCAAGCGGAAA
upper sequence: PP1S59_173V6.1 (Physcomitrella patens), 3'ss of exon 5
lower sequence: EFJ15774 (Selaginella moellendorffii), 3'ss of exon 6
attggtatcctaaaaaatacagctagtctgttggttttataattcgtgtttttgtgatacgtgatgaaataaatatcggctctgatgggaagtggtgcagGTTGCAGATTTTGGAGTTTCTGCTCAGCTGACTCGTACAATGTCCAAACGCAAG
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---------------------------------------------gtaactgcgtggtttagaaggttgtgattgta----ctcatattttataaaacagGTTGCAGATTTTGGTGTTTCTGCTCAGCTCACACGTACTGTGTCCAAGCGGAAAMapped 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|100383755|gb|BY969284.1|BY969284EST: CGGCTAATATACTGCTCACTGCAAATGGAGATGTTAAG GTTGCAGATTTTGGAGTTTCTGCTCAGCTGACTCGTACAATGTCCAAACGC
genomic: CGGCTAATATACTGCTCACTGCAAATGGAGATGTTAAGgtaagtttac ... agtggtgcagGTTGCAGATTTTGGAGTTTCTGCTCAGCTGACTCGTACAATGTCCAAACGC
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.gtgtttttgtgatacgtgatgaaataaatatcggctctgatgggaagtggtgcagGTTGCAGATTTTGGAGTTTCTGCTCAGCTGACTCGTACAATGTCCAAACGCAAG
ctctgat putative branch site (score: 4)
tgatgaaataaatat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
attggtatcctaaaaaatacagctagtctgttggttttataattcgtgtttttgtgatacgtgatgaaataaatatcggctctgatgggaagtggtgcagGTTGCAGATTTTGGAGTTTCTGCTCAGCTGACTCGTACAATGTCCAAACGCAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TCAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTGA