Sequence
atgc intronic sequence ATGC exonic sequence...ctcactttaccagttttctgcgcatgattgtttcaaggacttctgtatattaagctttgatcttgtaccaaaaactcagtttgatatgctgacccaacagGTGGCAGAACCTTTGAGAGCAATGGTAATGGGCGCACCTTTGGAAGATGCTCGTCATCTGGCACAACGATACGATCGCTTACGTCAAGAGGCTGAAAATC
Basic information
| species | Physcomitrella patens |
| transcript | PP1S34_169V6.1 |
| intron # | 5 |
| splice site | 3' |
| intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: PP1S34_169V6.1 (Physcomitrella patens), 3'ss of exon 5
lower sequence: LOC_Os10g36870.1 (Oryza sativa), 3'ss of exon 4
ctcactttaccagttttctgcgcatgattgtttcaaggacttctgtatattaagctttgatcttgtaccaaaa-actcagtttgatatgctgac-ccaacagGTGGCAGAACCTTTGAGAGCAATGGTAATGGGCGCACCTTTGGAAGATGCTCGTCATCTGGCACAACGATACGATCGCTTACGTCAAGAGGCTGAAAATC
| | | | ||| | || || || | |||||| || |||| | | | | || | || | | || ||||||||||||| ||||| || ||||| ||||| || ||||||||||||||||| ||||| || ||| ||||||| | | ||||| || || ||| |
-tgcaatgaatgccataatgcccttgcaaattgtaatcttgtgcatatattttactcaaatct-gcatgagactgttctgacatatggattaatatcattagGTGGCAGAACCGTTGAGGGCTATGGTGATGGGAGCTCCTTTGGAAGATGCTCGCCATCTTGCCCAAAGATACGACAGGATGCGTCAGGAAGCCGAAGCAC
upper sequence: PP1S34_169V6.1 (Physcomitrella patens), 3'ss of exon 5
lower sequence: Vv18s0001g13530.t01 (Vitis vinifera), 3'ss of exon 4
ctcactttaccagttttctgcgcatgattgtttcaaggacttc--tgtatattaagctttgatcttgtac------caaaaactcagtttgatatgctgacccaacagGTGGCAGAACCTTTGAGAGCAATGGTAATGGGCGCACCTTTGGAAGATGCTCGTCATCTGGCACAACGATACGATCGCTTACGTCAAGAGGCTGAAAATC
||| || | | ||| || || || || | | ||| | || ||| | | || | | |||| | || || ||||| | |||||| || ||||||||||||||||| || || ||||| |||||||| ||||| || |||||||| || | | || || |||||| ||
------tta--agacatatttacattatcattctaaattctccatttaatagtcagtttttcacctttataatgtgtagttatccagtgtttgattctttatttccagGTTGGAGAACCCTTAAGAGCAATGGTAATGGGAGCTCCCTTGGAGGATGCTCGACATCTTGCTCAACGATATGAGAGAATGCGAATGGAAGCTGAAGCTC
upper sequence: PP1S34_169V6.1 (Physcomitrella patens), 3'ss of exon 5
lower sequence: Vv10s0003g02590.t01 (Vitis vinifera), 3'ss of exon 4
-ctcactttaccagttttctgcgcatgattgtttcaaggacttctgtatatt-aagctttgatcttgtaccaaaaactcagtttgatatgctgacccaacagGTGGCAGAACCTTTGAGAGCAATGGTAATGGGCGCACCTTTGGAAGATGCTCGTCATCTGGCACAACGATACGATCGCTTACGTCAAGAGGCTGAAAATC
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ttctaaaggaacctttttctgttttccaat-ttttgttaactaattaagatagaagcattgattcctcaa-acattttttttttgtttttatatattttcagATTTTAGATCCTTTGAGAGCAATGGTCACTGGTGCTCCTTTGGAAGATGCCCGTCATCTAGCTCAACGTTATAGCCGAATGAGACATGAAGCTGAGACAC
upper sequence: PP1S34_169V6.1 (Physcomitrella patens), 3'ss of exon 5
lower sequence: EFJ27680 (Selaginella moellendorffii), 3'ss of exon 4
ctcactttaccagttttctgcgcatgattgtttcaaggacttctgtatattaagctttgatcttgtaccaaaaactcagtttgatatgctgacccaacagGTGGCAGAACCTTTGAGAGCAATGGTAATGGGCGCACCTTTGGAAGATGCTCGTCATCTGGCACAACGATACGATCGCTTACGTCAAGAGGCTGAAAATC
| | | ||| | || || || || | | || |||| | || ||| ||||||||||||| ||||| || || | |||||||| || |||||| |||| |||||||||||| | || || || || ||| |
------------------------------------------gtatgtcccaagg---agttttagacactgaaagcaagctatcttattg------tagGTTGGTGAGCCTCTGAGAGCAATGGTGATGGGTGCTCCACTCGAAGATGCACGCCATCTGACACAGCGATACGATCGCCTTCGGCAGGAAGCCGAAGTAC
upper sequence: PP1S34_169V6.1 (Physcomitrella patens), 3'ss of exon 5
lower sequence: EFJ32107 (Selaginella moellendorffii), 3'ss of exon 3
ctcactttaccagttttctgcgcatgattgtttcaaggacttctgtatattaagctttgatcttgtaccaaaaactcagtttgatatgctgacccaacagGTGGCAGAACCTTTGAGAGCAATGGTAATGGGCGCACCTTTGGAAGATGCTCGTCATCTGGCACAACGATACGATCGCTTACGTCAAGAGGCTGAAAATC
|||| || | | | || | || | | | | |||| || || ||||||||||| ||||| ||||| |||||||||||||| || || || |||||||||| || ||||| | || || ||||||||| |
-------------------------------------------------gtaagaagacattgtttgtgataagtt----ttaacaagt----cttgtagGTTGCTGAGCCTTTGAGAGCGATGGTGATGGGAGCACCTTTGGAAGACGCGCGGCACTTGGCACAACGCTATGATCGTCTGCGCCAGGAGGCTGAAGCGC
upper sequence: PP1S34_169V6.1 (Physcomitrella patens), 3'ss of exon 5
lower sequence: EFJ37738 (Selaginella moellendorffii), 3'ss of exon 3
ctcactttaccagttttctgcgcatgattgtttcaaggacttctgtatattaagctttgatcttgtaccaaaaactcagtttgatatgctgacccaacagGTGGCAGAACCTTTGAGAGCAATGGTAATGGGCGCACCTTTGGAAGATGCTCGTCATCTGGCACAACGATACGATCGCTTACGTCAAGAGGCTGAAAATC
||| | | || |||| || ||| | | | | ||||| || || ||||||||||| ||||| ||||| |||||||||||||| || || || |||||||||| || ||||| | || || ||||||||| |
--------------------------------------------gtaagaaagacatt--ctttgtgataagt------tttaacaagt----cttgcagGTTGCTGAGCCTTTGAGAGCGATGGTGATGGGAGCACCTTTGGAAGACGCGCGGCACTTGGCACAACGCTATGATCGTCTGCGCCAGGAGGCTGAAGCGC atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tatattaagctttgatcttgtaccaaaaactcagtttgatatgctgacccaacagGTGGCAGAACCTTTGAGAGCAATGGTAATGGGCGCACCTTTGGAAGATGCTCGTCATCTGGCACAACGATACGATCGCTTACGTCAAGAGGCTGAAAATC
tgctgac putative branch site (score: 2)
tttgatat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
ctcactttaccagttttctgcgcatgattgtttcaaggacttctgtatattaagctttgatcttgtaccaaaaactcagtttgatatgctgacccaacagGTGGCAGAACCTTTGAGAGCAATGGTAATGGGCGCACCTTTGGAAGATGCTCGTCATCTGGCACAACGATACGATCGCTTACGTCAAGAGGCTGAAAATC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGG
- - - - - - - - -ctgcgca
