Sequence
atgc intronic sequence ATGC exonic sequencegtgtgtatacttcgttttgtttgagtctattagtgtctagatcatattttattagtcttgtaggcgccctttcaagttcctgtgtgtgctaatttcatatccagcttggtgtcgactaatggtaatcagctctaaaaatttacctgcttggcttttgtaaccacagGATCACGATGGGTCTCATATCAAAGGATTGTTAATCAACTTCATCCACTCATTCTGGCCCTCGTTGCTCAAAATTCCATCATTCCTCGTGGAGTTCATCA
Basic information
species | Physcomitrella patens |
transcript | PP1S33_203V6.1 |
intron # | 8 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: PP1S33_203V6.1 (Physcomitrella patens), 3'ss of exon 8
lower sequence: GRMZM2G021270_T02 (Zea mays), 3'ss of exon 6
gtgtgtatacttcgttttgtttgagtctattagtgtctagatcatattttattagtcttgtaggcgccctttcaagttcctgtgtgtgctaatttcatatccagcttggtgtcgactaatggtaatcagctctaaaaatttacctgcttggcttttgtaaccacagGATCACGATGGGTCTCATATCAAAGGATTGTTAATCAACTTCATCCACTCATTCTGGCCCTCGTTGCTCAAAATTCCATCATTCCTCGTGGAGTTCATCA
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---------------------------------------------------------------------------------gtttg-gcaggcaacatctccaattttatatcaactaatgaaactcaagttttgtttgct-catgctttgacaccaaaatt-tagGATCATGATGGCTCCCACATTAAAGGGTTGCTGATCAACTTCATCCACTCATTCTGGCCGTCTCTTCTTAAAGTTCCATCTTTTTTGGTTGAGTTCATTA
upper sequence: PP1S33_203V6.1 (Physcomitrella patens), 3'ss of exon 8
lower sequence: AT3G23890.1 (Arabidopsis thaliana), 3'ss of exon 6
gtgtgtatacttcgttttgtttgagtctattagtgtctagatcatattttattagtcttgtaggcgccctttcaagttcctgtgtgtgctaatttcatatccagcttggtgtcgactaatggtaatcagctctaaaaatttacctgcttggcttttgtaaccacagGATCACGATGGGTCTCATATCAAAGGATTGTTAATCAACTTCATCCACTCATTCTGGCCCTCGTTGCTCAAAATTCCATCATTCCTCGTGGAGTTCATCA
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-----------------------------------------------------------------gtatgttaaaagtc---tactccctaactttacactcagtgcattattctatatggatatgttcttgacgaaatctccctctctaccttgtg------cagGATCATGATGGTTCTCATATAAAGGGTCTCTTAATCAATTTTATCCACTCTTTTTGGCCGTCGTTACTCCAGGTTCCATCATTCCTGGTTGAGTTTATAA
upper sequence: PP1S33_203V6.1 (Physcomitrella patens), 3'ss of exon 8
lower sequence: Vv13s0064g00560.t01 (Vitis vinifera), 3'ss of exon 6
gtgtgtatacttcgttttgtttgagtctattagtgtctagatcatattttattagtcttgtaggcgccctttcaagttcctgtgtgtgctaatttcatatccagcttggtgtcgactaatggtaatcagctctaaaaatttacctgcttggcttttgtaaccacagGATCACGATGGGTCTCATATCAAAGGATTGTTAATCAACTTCATCCACTCATTCTGGCCCTCGTTGCTCAAAATTCCATCATTCCTCGTGGAGTTCATCA
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--------------------------------------------------gttggccaaacaattccagttttc--ctgctttacttgcgactgttattggcctttgccaatagagtaatatgagtccttggttaacagtagtttattt--cttctcttac-acagGATCATGATGGCTCTCACATCAAAGGACTATTGATAAATTTCATTCATTCATTCTGGCCTTCACTGCTAAAAATTCCATCTTTCTTAGTTGAGTTCATAA atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tcgactaatggtaatcagctctaaaaatttacctgcttggcttttgtaaccacagGATCACGATGGGTCTCATATCAAAGGATTGTTAATCAACTTCATCCACTCATTCTGGCCCTCGTTGCTCAAAATTCCATCATTCCTCGTGGAGTTCATCA
ttgtaac putative branch site (score: 2)
cttttgt CT-rich tract
tctaaaaattta 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtgtgtatacttcgttttgtttgagtctattagtgtctagatcatattttattagtcttgtaggcgccctttcaagttcctgtgtgtgctaatttcatatccagcttggtgtcgactaatggtaatcagctctaaaaatttacctgcttggcttttgtaaccacagGATCACGATGGGTCTCATATCAAAGGATTGTTAATCAACTTCATCCACTCATTCTGGCCCTCGTTGCTCAAAATTCCATCATTCCTCGTGGAGTTCATCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GTGGAG