Sequence
atgc intronic sequence ATGC exonic sequence...cgagtgatttaggattgctgtactccgatgctcaatggcaaatttcgaaagcttcgaattttgaacgatttcggggaccttaaaatgtgtcgtatcgcagGTAAAGAGACATTTCAAGGACATTGGAGTACCAGCGGATGTGAAGTACATTGATCCTACCTACATGATTCGAGCATGTCGAGCCAATGCTTCTGACCGAA
Basic information
species | Physcomitrella patens |
transcript | PP1S114_31V6.1 |
intron # | 11 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: PP1S114_31V6.1 (Physcomitrella patens), 3'ss of exon 11
lower sequence: LOC_Os08g34050.1 (Oryza sativa), 3'ss of exon 11
-cgagtga-tttaggattgctgtactccgatgctca-atggcaaatttcgaaagcttcgaattttgaacgatttcggggaccttaaaatgtgtcgtatcgcagGTAAAGAGACATTTCAAGGACATTGGAGTACCAGCGGATGTGAAGTACATTGATCCTACCTACATGATTCGAGCATGTCGAGCCAATGCTTCTGACCGAA
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atagttgaacccaaggcttccctgcttttgtcttcccacgtttcttttctgtattgtcaatcataccatcataatagataacatcagttacaat---tttcagATTAAGATGCATTTCAAGGACATTGGTGTTCCTGCTGATGTAAAATACATTGATCCGACATATATGGTTCGGGCATGTCGTGCCAATGCATCTGATGCAA
upper sequence: PP1S114_31V6.1 (Physcomitrella patens), 3'ss of exon 11
lower sequence: LOC_Os10g26570.1 (Oryza sativa), 3'ss of exon 12
cgagtgatttaggattgctgtactccgatgctcaatggcaaatttcgaaagcttcgaattttgaacgatttcggggaccttaaaatgtgtcgtatcgcagGTAAAGAGACATTTCAAGGACATTGGAGTACCAGCGGATGTGAAGTACATTGATCCTACCTACATGATTCGAGCATGTCGAGCCAATGCTTCTGACCGAA
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-----gtttgtccatcgaatgaccttcac-cttgatgatgtat--caaaaa--tcacatgccaaaccaaatctaa----cttaaccgtgccatgccacagATCAAGGCCCATTTCAAGGAAATAGGAGTACATTCTGATGTGAAGTACATTGATCCTACATACATGGTCCGTGCTGTGCGTGCCAATGCATCCGATGCCA
upper sequence: PP1S114_31V6.1 (Physcomitrella patens), 3'ss of exon 11
lower sequence: LOC_Os09g24910.2 (Oryza sativa), 3'ss of exon 12
---cgagtgatttaggattgctgtactccgatgctcaatggcaaa-tttcgaaagcttcgaattttgaacgatttcggggaccttaaaatg-tgtcgtatcgcagGTAAAGAGACATTTCAAGGACATTGGAGTACCAGCGGATGTGAAGTACATTGATCCTACCTACATGATTCGAGCATGTCGAGCCAATGCTTCTGACCGAA
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tgtattctgctcctacattgctattgctctattctttatgatgttcttttgtgagctt---acttagtat--ttctgaataaatgacactgatatcgaattccagATTAAGAGTCATTTCAAGGACATCGGTGTTCCAGCTGATGTAAAATACATTGATCCGACATATATGGTCCGGGCCTGTCGTGCGAATGCATCTGATGCTA
upper sequence: PP1S114_31V6.1 (Physcomitrella patens), 3'ss of exon 11
lower sequence: GRMZM2G139360_T06 (Zea mays), 3'ss of exon 8
cgagtgatttaggattgctgtactc-cgatgctc-aatggcaaatttcgaaagcttcgaattttgaacgatttcggggacctta---aaatgtgt-cgtatcgcagGTAAAGAGACATTTCAAGGACATTGGAGTACCAGCGGATGTGAAGTACATTGATCCTACCTACATGATTCGAGCATGTCGAGCCAATGCTTCTGACCGAA
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------atttgcagctgctaaaccaatgattttccagtttccttctgttaccattgtccttttcagaagttatcaatcatataatggaattgcctgcacttttcagATTAAGATGCATTTCAAGGACATTGGTGTTCCAGCTGACGTGAAATACATCGATCCAACTTACATGGTTCGTGCATGCCGTGCCAACGCATCTGATGCAA
upper sequence: PP1S114_31V6.1 (Physcomitrella patens), 3'ss of exon 11
lower sequence: Vv14s0108g00540.t01 (Vitis vinifera), 3'ss of exon 12
-----cgagtgatttaggattgctgtactccgatgctcaatggcaaatttcgaaagcttcgaattttg--aacgatttcggggaccttaaaatgtgtcgtatcgcagGTAAAGAGACATTTCAAGGACATTGGAGTACCAGCGGATGTGAAGTACATTGATCCTACCTACATGATTCGAGCATGTCGAGCCAATGCTTCTGACCGAA
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gttatagtctcatcttacaaggcagcacttgtattttcttccattctcttccatattcttgcattttcttgatgatagtgatgggctcacacttcttca----acagATCAAGAAACATTTTAGGAGGATTGGCGTTCCAGCTGATGTTAAATACATTGATCCCACTTATATGATTCGAGCGTGTCGAGCAAATGCATCTGATGCTGMapped 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|162189876|gb|FC365579.1|FC365579EST: CGTCGGGAAACCCAATCTTAGGAGACATTGGCGTACACCTCACAAAAGAG GTAAAGAGACATTTCAAGGACATTGGAGTACCAGCGGATGTGAAGTACATT
genomic: CGTCGGGAAACCCAATCTTAGGAGACATTGGCGTACACCTCACAAAAGAGgttagattgc ... cgtatcgcagGTAAAGAGACATTTCAAGGACATTGGAGTACCAGCGGATGTGAAGTACATT
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.cgaaagcttcgaattttgaacgatttcggggaccttaaaatgtgtcgtatcgcagGTAAAGAGACATTTCAAGGACATTGGAGTACCAGCGGATGTGAAGTACATTGATCCTACCTACATGATTCGAGCATGTCGAGCCAATGCTTCTGACCGAA
aattttgaa 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
cgagtgatttaggattgctgtactccgatgctcaatggcaaatttcgaaagcttcgaattttgaacgatttcggggaccttaaaatgtgtcgtatcgcagGTAAAGAGACATTTCAAGGACATTGGAGTACCAGCGGATGTGAAGTACATTGATCCTACCTACATGATTCGAGCATGTCGAGCCAATGCTTCTGACCGAA
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