Sequence
atgc intronic sequence ATGC exonic sequencegtacgtcacctgcttgcatgacctattggtgtgtggaattgtccatcttcccaactattcgttctcgttcgcattctgatccgattgagattgcgctggtatgtttgccacagGAGCTGAAGGGTAACATCCGCGTATTTTGTAGAGTTAGACCTCTTATGGTTGAGGAGGACGAAGGAAACGAGTCCCCTTCCGTGCAATTCCCGTCCTCTA
Basic information
species | Physcomitrella patens |
transcript | PP1S87_179V6.1 |
intron # | 8 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: PP1S87_179V6.1 (Physcomitrella patens), 3'ss of exon 8
lower sequence: GRMZM2G436981_T01 (Zea mays), 3'ss of exon 8
gtacgtcacctgcttgcatgacctattggtgtgtggaattgtccatcttcccaactattcgttctcgttcgcattctgatccgattgagattgcgctggtatgtttgccacagGAGCTGAAGGGTAACATCCGCGTATTTTGTAGAGTTAGACCTCTTATGGTTGAGGAGGACGAAGGAA-ACGAGTCCCCTTCCGTGCAATTCCCGTCCTCTA
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------------------------------gtatggaattctct-tattctcaaagatccagttt-atataaatatatgttatgtggctattcctgaatttggttctttgcagGAGTTGAAGGGAAACATCAGAGTATTTTGTAGAGTTAGGCCTTTGCTGCCAAATGAATCAGGAGCAGTATCATATCCAAAGAATGGAGAAAACTTAGGCC-
upper sequence: PP1S87_179V6.1 (Physcomitrella patens), 3'ss of exon 8
lower sequence: EFJ33133 (Selaginella moellendorffii), 3'ss of exon 8
gtacgtcacctgcttgcatgacctattggtgtgtggaattgtccatcttcccaactattcgttctcgttcgcattctgatccgattgagattgcgctggtatgtttgccacagGAGCTGAAGGGTAACATCCGCGTATTTTGTAGAGTTAGACCTCTTATGGTTGAGGAGGACGAAGGAAACGAGTCCCCTTCCGTGCAATTCCCGTCCTCTA-
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------------------------------------------------------------gttcgcactt---ttctgtttttatc-acctaaggcaaacagtgatgttacagGAGCTGAAGGGGAACATTCGTGTATTCTGTAGAGTAAGACCACTTTTACCCGATGAAAACGACG-AATCATCGACTCTGATCAGCTATCCAGGCGAGGAGG
upper sequence: PP1S87_179V6.1 (Physcomitrella patens), 3'ss of exon 8
lower sequence: EFJ27367 (Selaginella moellendorffii), 3'ss of exon 7
gtacgtcacctgcttgcatgacctattggtgtgtggaattgtccatcttcccaactattcgttctcgttcgcattctgatccgattgagattgcgctggtatgtttgccacagGAGCTGAAGGGTAACATCCGCGTATTTTGTAGAGTTAGACCTCTTATGGTTGAGGAGGACGAAGGAAACGAGTCCCCTTCCGTGCAATTCCCGTCCTCTA-
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------------------------------------------------------------gttcgcgctt---ttctgtttttatc-acctaaggcaaacagtgatgttacagGAGCTGAAGGGGAACATTCGTGTATTCTGTAGAGTAAGACCACTTTTACCCGATGAAAACGACG-AATCATCGACGCTGATCAGCTATCCAGGCGAGGAGG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tcgttctcgttcgcattctgatccgattgagattgcgctggtatgtttgccacagGAGCTGAAGGGTAACATCCGCGTATTTTGTAGAGTTAGACCTCTTATGGTTGAGGAGGACGAAGGAAACGAGTCCCCTTCCGTGCAATTCCCGTCCTCTA
ttctgat putative branch site (score: 3)
tatgttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtacgtcacctgcttgcatgacctattggtgtgtggaattgtccatcttcccaactattcgttctcgttcgcattctgatccgattgagattgcgctggtatgtttgccacagGAGCTGAAGGGTAACATCCGCGTATTTTGTAGAGTTAGACCTCTTATGGTTGAGGAGGACGAAGGAAACGAGTCCCCTTCCGTGCAATTCCCGTCCTCTA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAA