Sequence
atgc intronic sequence ATGC exonic sequencegtagagggttacggaaataatttcgtgcactttcctaggttatgttcaaagttttagtttgggactcacatgtcttttgtgtttcctccgttgcttatgaagtttttaatatgtgcagATCCACTTTGTGATTTCAAAGCCTGATGTGTTCAAGAGCCTGGTCTCAGACACACATAATCTATGGAGAGGCTAAGATCGAGGACTTGAGTTCTCAGCTT
Basic information
species | Physcomitrella patens |
transcript | PP1S9_207V6.1 |
intron # | 1 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: PP1S9_207V6.1 (Physcomitrella patens), 3'ss of exon 1
lower sequence: EFJ23805 (Selaginella moellendorffii), 3'ss of exon 3
gtagagggttacggaaataatttcgtgcactttcctaggttatgttcaaagttttagtttgggactcacatgtcttttgtgtttcctccgttgcttatgaagtttttaatatgtgcagATCCACTTTGTGATTTCAAAGCCTGATGTGTTCAAGAGCCTGGTCTCAGACAC--ACATAATCTATGGAGAGGCTAAGATCGAGGACTTGAGTTCTCAGCTT
||| || ||| | || | | | || || | || ||| || | ||||| | |||||||| || ||||| || ||||||||||||| || || ||||| |||| |||| ||| ||||| |||||||||||||||||||| ||||
----------------------------------------------gtaagcttgcgttggtagatcgaagagaatagagactaacttcgcttct-----ggttctt------tccagATACTGTTTGTGATCTCCAAGCCCGACGTGTTCAAGAGCCCGGCATCCGACACTCACATCATCTTTGGCGAGGCCAAGATCGAGGACTTGAGTTCCCAGC--
upper sequence: PP1S9_207V6.1 (Physcomitrella patens), 3'ss of exon 1
lower sequence: EFJ21445 (Selaginella moellendorffii), 3'ss of exon 1
gtagagggttacggaaataatttcgtgcactttcctaggttatgttcaaagttttagtttgggactcacatgtcttttgtgtttcctccgttgcttatgaagtttttaatatgtgcagATCCACTTTGTGATTTCAAAGCCTGATGTGTTCAAGAGCCTGGTCTCAGACAC--ACATAATCTATGGAGAGGCTAAGATCGAGGACTTGAGTTCTCAGCTT
||| || || || | | | || | || || | ||| ||| || | ||||| | || ||||| || ||||| || ||||||||||||| || || ||||| |||| |||| ||| ||||| |||||||||||||||||||| ||||
----------------------------------------------gtaagcttgcgtagtagatgaaagagaatagagt-ctaacttcgctcctt-----gttctt------tccagATACTGTTCGTGATCTCCAAGCCCGACGTGTTCAAGAGCCCGGCATCCGACACTCACATCATCTTTGGCGAGGCCAAGATCGAGGACTTGAGTTCCCAGC-- atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.actcacatgtcttttgtgtttcctccgttgcttatgaagtttttaatatgtgcagATCCACTTTGTGATTTCAAAGCCTGATGTGTTCAAGAGCCTGGTCTCAGACACACATAATCTATGGAGAGGCTAAGATCGAGGACTTGAGTTCTCAGCTT
ttatgaagtttttaat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtagagggttacggaaataatttcgtgcactttcctaggttatgttcaaagttttagtttgggactcacatgtcttttgtgtttcctccgttgcttatgaagtttttaatatgtgcagATCCACTTTGTGATTTCAAAGCCTGATGTGTTCAAGAGCCTGGTCTCAGACACACATAATCTATGGAGAGGCTAAGATCGAGGACTTGAGTTCTCAGCTT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TCAGCT