Sequence
atgc intronic sequence ATGC exonic sequence...ggcactagattctatatgagtgatattctatttccgggcagtcaagtcgtgcactggaggtagactgattggcacatgatattttgagcgggggctgcagTGATGTGGTGCATATGGCAAGCTACGCACCCCTCTTTGTTAATGACAACGACAGAAG
Basic information
species | Physcomitrella patens |
transcript | PP1S317_21V6.1 |
intron # | 13 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: PP1S317_21V6.1 (Physcomitrella patens), 3'ss of exon 13
lower sequence: GRMZM2G097277_T01 (Zea mays), 3'ss of exon 13
ggcactagattctatatgagtgatattctatttccgggcagtcaagtcgtgcactggaggtagactgattggcacatgatattttgagcgggg-gctgcagTGATGTGGTGCATATGGCAAGCTACGCACCCCTCTTTGTTAATGACAACGACAGAAG
|| | | |||| | |||| | ||| ||| || || | | || | |||| | ||||||||||||||| | |||||||||| |||||||| ||||| |||||||| || | ||
--------gttagctgt-agtgtacccgttcttcctcattttagagttctgccaaaattaaagcatgttgcagatataactgtttgtttgttctactgcagTGATGTGGTTGAGATGGCAAGCTGTGCACCCCTTTTTGTAAATGACAATGATCGCAG
upper sequence: PP1S317_21V6.1 (Physcomitrella patens), 3'ss of exon 13
lower sequence: EFJ22660 (Selaginella moellendorffii), 3'ss of exon 13
ggcactagattctatatgagtgatattctatttccgggcagtcaagtcgtgcactggaggtagactgattggcacatgatattttgagcgggggctgcagTGATGTGGTGCATATGGCAAGCTACGCACCCCTCTTTGTTAATGACAACGACAGAAG
| | || | || || | || | | | | ||||| | |||||||| ||||||||| |||||||||| ||||||||||| ||| ||||||| | ||
-------------------------------------------gtaacttccattagaaataaat---ttcgagcgtaactttttgtac------catagTGATGTTGTGCATATGACAAGCTACGCTCCCCTCTTTGTAAATAACAACGATCGCAG
upper sequence: PP1S317_21V6.1 (Physcomitrella patens), 3'ss of exon 13
lower sequence: EFJ11809 (Selaginella moellendorffii), 3'ss of exon 13
ggcactagattctatatgagtgatattctatttccgggcagtcaagtcgtgcactggaggtagactgattggcacatgatattttgagcgggggctgcagTGATGTGGTGCATATGGCAAGCTACGCACCCCTCTTTGTTAATGACAACGACAGAAG
| | || | || || || | | | ||| | | ||||||||| || |||||| |||||||||| ||||||||||| ||| ||||||| | ||
-------------------------------------------gtaacttccattagaaaaagtt---ttcgagctaactttttcta-------ccacagTGATGTTGTACATATGACAAGCTACGCTCCCCTCTTTGTAAATAACAACGATCGCAG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.gtcgtgcactggaggtagactgattggcacatgatattttgagcgggggctgcagTGATGTGGTGCATATGGCAAGCTACGCACCCCTCTTTGTTAATGACAACGACAGAAG
gactgat putative branch site (score: 3)
atgatatttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
ggcactagattctatatgagtgatattctatttccgggcagtcaagtcgtgcactggaggtagactgattggcacatgatattttgagcgggggctgcagTGATGTGGTGCATATGGCAAGCTACGCACCCCTCTTTGTTAATGACAACGACAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - cacatga