Sequence
atgc intronic sequence ATGC exonic sequencegtaggaactgcttttgtcatggtttttcagcacggagattaactcgtgagtgcaatctaataattctggacgtttttgtgtacttattgcctattaaatcgtacttattagataatatgttaatacgcagATATGTGGCGCCTGAATACGCGATGACAGGCCACCTCCTAGTGAAGAGCGACGTGTACAGCTATGGGGTGGTTCTTCTTGAGCTTCTCTCAGGGAGGATG
Basic information
species | Physcomitrella patens |
transcript | PP1S293_24V6.1 |
intron # | 7 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: PP1S293_24V6.1 (Physcomitrella patens), 3'ss of exon 7
lower sequence: LOC_Os04g43020.1 (Oryza sativa), 3'ss of exon 7
gtaggaactgcttttgtcatggtttttcagcacggagattaactcgtgagtg-caatctaataattctggacgtttttgtgtacttattgcctattaaatcgtacttattagataatatgttaatacgcagATATGTGGCGCCTGAATACGCGATGACAGGCCACCTCCTAGTGAAGAGCGACGTGTACAGCTATGGGGTGGTTCTTCTTGAGCTTCTCTCAGGGAGGATG
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---gaaatcgtattagcaaataatta-----acggcgatgatattgtgaataataagctgaaaa----gaaagttt------aacttttg---atcgatttctttttgtca----------tggtcttcagGTACGTTGCCCCGGAGTATGCGATGACCGGGCATCTCCTGGTGAAAAGCGACGTGTACAGCTACGGTGTCGTGCTGCTGGAGCTCCTCTCGGGGAGGAAG
upper sequence: PP1S293_24V6.1 (Physcomitrella patens), 3'ss of exon 7
lower sequence: LOC_Os01g51290.1 (Oryza sativa), 3'ss of exon 12
gtaggaactgcttttgtcatggtttttcagcacggagattaactcgtgagtgc-aatctaataattctggacgtttttgtgtacttattgcctattaaatcgtacttattagataatatgttaatacgcagATATGTGGCGCCTGAATACGCGATGACAGGCCACCTCCTAGTGAAGAGCGACGTGTACAGCTATGGGGTGGTTCTTCTTGAGCTTCTCTCAGGGAGGATG
|| ||| |||| | | | | | |||| || | || || | | |||| || | | || ||||| || ||||||||||| ||||| || || || ||||| ||||| || || ||||||||||| || || || ||||||||||| | || ||||
---------------------------------------------gtaagttttgatctgaaattattatcttactacctgtagttggttaacatcc--tcaccttaaaaagattatgaactctttt-tagGTATGTTGCTCCTGAATACGCAATGACTGGGCATCTTCTAGTAAAGAGTGATGTCTACAGCTATGGTGTCGTCCTCCTTGAGCTTCTTACCGGAAGGAAA
upper sequence: PP1S293_24V6.1 (Physcomitrella patens), 3'ss of exon 7
lower sequence: LOC_Os01g09860.1 (Oryza sativa), 3'ss of exon 13
gtaggaactgcttttgtcatggtttttcagcacggagattaactcgtgagtgcaatctaataattctggacgtttttgtgtacttattgcctattaaatcgtacttattagataatatgttaatacgcagATATGTGGCGCCTGAATACGCGATGACAGGCCACCTCCTAGTGAAGAGCGACGTGTACAGCTATGGGGTGGTTCTTCTTGAGCTTCTCTCAGGGAGGATG
||| | ||| | || ||| | || | | | | ||| | || || || || | || | | ||||||||| || || || || || |||||||| || ||||| || |||||||| |||||||||||||| || || | |||||||| ||| | || || | |
-------------------------------------------gtatgaatcatatccctcatccctctgtgttctgatggaatcacaattt-ctaatgcata---atatgactatgtctttcttctcagATATGTTGCACCGGAGTATGCCATGACAGGACATCTCCTTGTCAAGAGCGATGTGTACAGCTATGGAGTAGTGTTGCTTGAGCTCCTCACCGGTAGAAAG
upper sequence: PP1S293_24V6.1 (Physcomitrella patens), 3'ss of exon 7
lower sequence: GRMZM2G330298_T01 (Zea mays), 3'ss of exon 6
gtaggaactgcttttgtcatggtttttcagcacggagattaactc-gtgagtgcaatctaataattctggacgtttttgtgtacttattgcctattaaatcgtacttattagataatatgttaata---cgcagATATGTGGCGCCTGAATACGCGATGACAGGCCACCTCCTAGTGAAGAGCGACGTGTACAGCTATGGGGTGGTTCTTCTTGAGCTTCTCTCAGGGAGGATG
| | ||| || | | | | |||| || |||| | | || | | | | || || || || || ||| | || | || ||| | || ||| | || |||||||| || ||||| ||||| || ||||| ||||| || || |||||||| || || ||||||||||||||||| |||||||||
---------------------------------gtatgctaaatctgaaattactatctt-tacttct-----tcatagttgattcaatacc-atcaactcata-ttacaaaattctg-gtcaatttctcttagGTATCTTGCTCCTGAATATGCAATGACTGGCCATCTTCTAGTAAAGAGTGATGTTTACAGCTACGGTGTTGTTCTTCTTGAGCTTCTTACAGGGAGGAAA atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ttgtgtacttattgcctattaaatcgtacttattagataatatgttaatacgcagATATGTGGCGCCTGAATACGCGATGACAGGCCACCTCCTAGTGAAGAGCGACGTGTACAGCTATGGGGTGGTTCTTCTTGAGCTTCTCTCAGGGAGGATG
tgttaat putative branch site (score: 3)
tattaaatcgtactta 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaggaactgcttttgtcatggtttttcagcacggagattaactcgtgagtgcaatctaataattctggacgtttttgtgtacttattgcctattaaatcgtacttattagataatatgttaatacgcagATATGTGGCGCCTGAATACGCGATGACAGGCCACCTCCTAGTGAAGAGCGACGTGTACAGCTATGGGGTGGTTCTTCTTGAGCTTCTCTCAGGGAGGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGCTT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGGATG