Sequence
atgc intronic sequence ATGC exonic sequencegttcgatgttgtctcacgactcggcgaaatactttcctgaaatttttgcccatccttctgaggcattgttgttcattaaatcggcggattaatggttgtggtggtttaaaattttagtaccacgattgttaatattattaccgactttgtacagATTCAAGCTGCATTTCGTACTGACGAGATCCGACGGTCACAGCCAACACCCCAGGATGAGATGCGTGCAGGCATGAGTTACTTCCACGAGACTATCTGGA
Basic information
species | Physcomitrella patens |
transcript | PP1S169_156V6.1 |
intron # | 3 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: PP1S169_156V6.1 (Physcomitrella patens), 3'ss of exon 3
lower sequence: EFJ13502 (Selaginella moellendorffii), 3'ss of exon 3
gttcgatgttgtctcacgactcggcgaaatactttcctgaaatttttgcccatccttctgaggcattgttgttcattaaatcggcggattaatggttgtggtggtttaaaattttagtaccacgattgttaata--ttattaccgactttgt----acagATTCAAGCTGCATTTCGTACTGACGAGATCCGACGGTCACAGCCAACACCCCAGGATGAGATGCGTGCAGGCATGAGTTACTTCCACGAGACTATCTGGA
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--------------------------------------------------------------------------------------------------------gtaagtgtttttttgtctcgtttgtagataaaccaatgctggctccattctcgcagATTCAAGCTGCTTTTCGAACTGATGAAATAAGACGTGCGCCCCCAACCCCGCAGGACGAGATGCGTGCCGGGATGAGCTACTTTCACGAGACAATCTGGA
upper sequence: PP1S169_156V6.1 (Physcomitrella patens), 3'ss of exon 3
lower sequence: EFJ19066 (Selaginella moellendorffii), 3'ss of exon 3
gttcgatgttgtctcacgactcggcgaaatactttcctgaaatttttgcccatccttctgaggcattgttgttcattaaatcggcggattaatggttgtggtggtttaaaattttagtaccacgattgttaata--ttattaccgactttgt----acagATTCAAGCTGCATTTCGTACTGACGAGATCCGACGGTCACAGCCAACACCCCAGGATGAGATGCGTGCAGGCATGAGTTACTTCCACGAGACTATCTGGA
| | |||| | | || |||| ||| | | | | || | |||||||||||||| ||||| ||||| || || |||| | | ||||| || ||||| ||||||||||| || ||||| ||||| |||||||| |||||||
--------------------------------------------------------------------------------------------------------gtaagtgtttttttgtctcgtttgtagataaaccaatgctggctccattctcgcagATTCAAGCTGCTTTTCGAACTGATGAAATAAGACGTGCGCCACCAACCCCGCAGGACGAGATGCGTGCCGGGATGAGCTACTTTCACGAGACAATCTGGA
upper sequence: PP1S169_156V6.1 (Physcomitrella patens), 3'ss of exon 3
lower sequence: EFJ06433 (Selaginella moellendorffii), 3'ss of exon 3
gttcgatgttgtctcacgactcggcgaaatactttcctgaaatttttgcccatccttctgaggcattgttgttcattaaatcggcggattaatggttgtggtggtttaaaattttagtaccacgattgttaatattattaccgactttgtacagATTCAAGCTGCATTTCGTACTGACGAGATCCGACGGTCACAGCCAACACCCCAGGATGAGATGCGTGCAGGCATGAGTTACTTCCACGAGACTATCTGGA
| | || | | || ||||| | | || | || | || |||| ||| | ||||| || ||||| ||||||||||| | || ||| |||||||| |||||||||||||| || || ||||| ||||||||||| || |||||||
-------------------------------------------------------------------------------gtaagtccatccacacacaccgcgg-------gattagtttcgtgcttat-aacaccgtt-ttgactgc---cagGTCCAAGCGGCCTTTCGGACTGACGAGATTAGGCGCACACCACCAACACCTCAGGATGAGATGCGAGCCGGAATGAGCTACTTCCACGAAACAATCTGGA atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ggtggtttaaaattttagtaccacgattgttaatattattaccgactttgtacagATTCAAGCTGCATTTCGTACTGACGAGATCCGACGGTCACAGCCAACACCCCAGGATGAGATGCGTGCAGGCATGAGTTACTTCCACGAGACTATCTGGA
tgttaat putative branch site (score: 3)
attgttaatattatta 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gttcgatgttgtctcacgactcggcgaaatactttcctgaaatttttgcccatccttctgaggcattgttgttcattaaatcggcggattaatggttgtggtggtttaaaattttagtaccacgattgttaatattattaccgactttgtacagATTCAAGCTGCATTTCGTACTGACGAGATCCGACGGTCACAGCCAACACCCCAGGATGAGATGCGTGCAGGCATGAGTTACTTCCACGAGACTATCTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGATG