Sequence
atgc intronic sequence ATGC exonic sequencegtatcacatgattcgtctggattattgtggagttatttgaagatgctggtgtcctactgactacgtccaaatatgctaattgctgttgtcataagagaaatgaagataagttctgcgagattctaactagagactaaaatcaatgtgtcgtcttgtagGCGTATGAGAAGTCAGAAGATCCAATCTATGTTTTGGAGAATAATATTCCGATTGATCCACAATACTACTTGGAAAACCAGCTGAGTAAG
Basic information
species | Physcomitrella patens |
transcript | PP1S54_271V6.1 |
intron # | 25 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: PP1S54_271V6.1 (Physcomitrella patens), 3'ss of exon 25
lower sequence: LOC_Os11g08330.1 (Oryza sativa), 3'ss of exon 25
gtatcacatgattcgtctggattattgtggagttatttgaagatgctggtgtcctactgactacgtccaaatatgctaattgctgttgtcataagagaaatgaagataagttctgcgagattctaactagagactaaaatcaatgtgtcgtcttgtagGCGTATGAGAAGTCAGAAGATCCAATCTATGTTTTGGAGAATAATATTCCGATTGATCCACAATACTACTTGGAAAACCAGCTGAGTAAG
|| ||| | || | | ||| |||| ||| | || || || | | || | || | ||||| || |||||||||| ||||||| |||||||||||| || ||||||||||| ||||| || || || ||||| ||||||||| | || ||||| | || ||
------------------------------------------------------------gtaaacttgaatgtact---ttcaattgc----agagtcatgtatttatcttgtg-atggtgatagtttga---tgaaatc----cttcttcttgtagGCATATGAGAGGTCAGAAGATCCTATTTATGTTTTGGATAATAACATACCAATAGATCCCCAATACTACCTTGAGAACCAAATCAGCAAA
upper sequence: PP1S54_271V6.1 (Physcomitrella patens), 3'ss of exon 25
lower sequence: GRMZM2G115245_T01 (Zea mays), 3'ss of exon 9
gtatcacatgattcgtctggattattgtggagttatttgaagatgctggtgtcctactgactacgtccaaatatgctaattgctgttgtcataagagaaatgaagataagttctgcgagattctaactagagactaaaatcaatgtgtcgtcttgtagGCGTATGAGAAGTCAGAAGATCCAATCTATGTTTTGGAGAATAATATTCCGATTGATCCACAATACTACTTGGAAAACCAGCTGAGTAAG
||| || | | | | || | | | || | | || | | || | || |||| |||||||| ||||||||||| || ||||||||||| |||||||| || |||||||| ||||||||| | || ||||| | || |||
---------------------------------------------------------------------------gtaaaaaagtctgcatcatgtgctgcggtattatctgtcataatgtggtagtgtgtttgatacatttgtctttctgcatgcagGCATATGAGAAATCAGAAGATCCGATTTATGTTTTGGACAATAATATACCCATTGATCCTCAATACTACCTTGAGAACCAAATTAGCAAG
upper sequence: PP1S54_271V6.1 (Physcomitrella patens), 3'ss of exon 25
lower sequence: EFJ15224 (Selaginella moellendorffii), 3'ss of exon 24
gtatcacatgattcgtctggattattgtggagttatttgaagatgctggtgtcctactgactacgtccaaatatgctaattgctgttgtcataagagaaatgaagataagttctgcgagattctaactagagactaaaatcaatgtgtcgtcttgtagGCGTATGAGAAGTCAGAAGATCCAATCTATGTTTTGGAGAATAATATTCCGATTGATCCACAATACTACTTGGAAAACCAGCTGAGTAAG
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------------------------------------------------------------------------------------------------gttgtatgtttttgttcattgatctgctgtctc----tttaaat---tatctcctttcgcagGCATATGAGCGGTCTGAGGATCCAATCTATGTCTTGGAAAATAACATTCCCATCGATCCTCAGTACTATCTGGAAAATCAGCTGAGTAAG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.agataagttctgcgagattctaactagagactaaaatcaatgtgtcgtcttgtagGCGTATGAGAAGTCAGAAGATCCAATCTATGTTTTGGAGAATAATATTCCGATTGATCCACAATACTACTTGGAAAACCAGCTGAGTAAG
tcgtctt CT-rich tract
taaaatcaat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtatcacatgattcgtctggattattgtggagttatttgaagatgctggtgtcctactgactacgtccaaatatgctaattgctgttgtcataagagaaatgaagataagttctgcgagattctaactagagactaaaatcaatgtgtcgtcttgtagGCGTATGAGAAGTCAGAAGATCCAATCTATGTTTTGGAGAATAATATTCCGATTGATCCACAATACTACTTGGAAAACCAGCTGAGTAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTGA