Sequence
atgc intronic sequence ATGC exonic sequence...tggagtaggaaaactggattttagaatgcttaagtggcagcctttcgtggaagattaaaatgcagtgtgatcaagattgacaagcaatctgcttttgcagATTTGATCGCGACTGGAAAAAGATTGAAGCTTTCGTTGGTTCTAAGACAGTCATACAG
Basic information
species | Physcomitrella patens |
transcript | PP1S160_6V6.1 |
intron # | 2 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: PP1S160_6V6.1 (Physcomitrella patens), 3'ss of exon 2
lower sequence: LOC_Os06g01670.1 (Oryza sativa), 3'ss of exon 1
---tggagtaggaaaactggattttagaatgcttaagtggcagcctttcgtggaagattaaaatgcagtgtgatcaagattgacaagcaatctgcttttgcagATTTGATCGCGACTGGAAAAAGATTGAAGCTTTCGTTGGTTCTAAGACAGTCATACAG
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ttatcttgtggcaaacattacgagtggggttttaccacaactgaaaa--atggttccttcctacttattctttgcattctttacttgct-tttactataacagGTTTGATCGTGATTGGAAAAAGATTGAAGCATATGTTGGCTCTAAGACTGTAATACAG
upper sequence: PP1S160_6V6.1 (Physcomitrella patens), 3'ss of exon 2
lower sequence: GRMZM2G135052_T01 (Zea mays), 3'ss of exon 1
tggagtaggaaaactggattttagaatgctt-aagtggcagcctttcgtggaagattaaaatgcagtgtgatcaagattgacaagcaatctgcttttgcagATTTGATCGCGACTGGAAAAAGATTGAAGCTTTCGTTGGTTCTAAGACAGTCATACAG
| | | | | || |||||||| | | || || | | | | | | || | | | || | | || | | | | ||| ||||| || |||||||||||||||||||| | ||||| || |||||||| ||||||
tttaagggcatttcatacttgtagaatgcctcatgtcaca-catctggagcagctttcttacatattatgctataaatccttctttcttttcgtgtaacagCTTTGACCGTGACTGGAAAAAGATTGAAGCATATGTTGGCTCCAAGACAGTAATACAG
upper sequence: PP1S160_6V6.1 (Physcomitrella patens), 3'ss of exon 2
lower sequence: GLYMA16G03640.1 (Glycine max), 3'ss of exon 1
tggagtaggaaaactggattttagaatgcttaagtggcagcct-ttcgtggaagattaaaatgcagtgtgatcaagattgacaagcaatctgctt-ttgcagATTTGATCGCGACTGGAAAAAGATTGAAGCTTTCGTTGGTTCTAAGACAGTCATACAG
| | | | | || ||| |||| | | || || | ||| | | | | || | || || |||||||||||| |||||||||||||||||||| || |||||||| || ||||| || |||
caaaaccagtatatgtaacaata--atgattaatttatgatttatttgtatatttttacttttttttttctgtgtttctcacttttgcttgactaattccagATTTGATCGGGACTGGAAAAAGATTGAAGCATTTGTTGGTTCAAAAACAGTTATCCAG
upper sequence: PP1S160_6V6.1 (Physcomitrella patens), 3'ss of exon 2
lower sequence: GLYMA07G07200.1 (Glycine max), 3'ss of exon 1
tggagtaggaaaactggattttagaatgctta-agtggcagcctttcgtggaagattaaaatgcagtgtgatcaagattgacaagcaatctgctt-ttgcagATTTGATCGCGACTGGAAAAAGATTGAAGCTTTCGTTGGTTCTAAGACAGTCATACAG
| | | | || | | ||| | | || | || || || | | | | || | | || || |||||||||||| |||||||||||||||||||| || |||||||| || ||||| || |||
--ttccaaaaccagtatatgtaacaatattgatggtttatgatttgtttgtttacttttacctttttttttgtgtttctcactttcgcttgactaatttcagATTTGATCGGGACTGGAAAAAGATTGAAGCATTTGTTGGTTCAAAAACAGTTATCCAG
upper sequence: PP1S160_6V6.1 (Physcomitrella patens), 3'ss of exon 2
lower sequence: GLYMA20G30250.1 (Glycine max), 3'ss of exon 1
--tggagtaggaaaactggattt----tagaatgcttaagtggcagcctttcgtggaagattaaaatgcagtgtgatcaagattgacaagcaatctgcttttgcagATTTGATCGCGACTGGAAAAAGATTGAAGCTTTCGTTGGTTCTAAGACAGTCATACAG
| || || ||| | | || | ||| || ||||| | | | | | || | | | | | || |||| | ||||||||| || |||||||||||||||||||| || ||||| || ||||||||||| |||
atttaagctatttgtttgtttttcccttttatggccttggtgccatccttttgcattatctcatattgttttttttttttgttcctt---cattctgtat---cagATTTGACCGTGACTGGAAAAAGATTGAAGCATTTGTTGGATCAAAGACAGTCATCCAG
upper sequence: PP1S160_6V6.1 (Physcomitrella patens), 3'ss of exon 2
lower sequence: GLYMA10G37520.1 (Glycine max), 3'ss of exon 1
tggagtaggaaaactggattttagaatgcttaagtggcagcctttcgtggaagattaaaatgcagtgtgatcaagattgacaagcaatctgcttttgcagATTTGATCGCGACTGGAAAAAGATTGAAGCTTTCGTTGGTTCTAAGACAGTCATACAG
| ||| ||| ||| | | || || | | || |||| | | | || | | || | ||||||||| || |||||||||||||||||||| || ||||| || |||||||| || |||
tacagtgtcaaattaagataatcgtttgttttcccttttctggccttagtatcatccttttgcattatctcattgttttgtattttcattctttatccagATTTGACCGTGACTGGAAAAAGATTGAAGCATTTGTTGGATCAAAGACAGTTATCCAG
upper sequence: PP1S160_6V6.1 (Physcomitrella patens), 3'ss of exon 2
lower sequence: AT5G52660.2 (Arabidopsis thaliana), 3'ss of exon 1
-tggagtaggaaaactggattttagaatgcttaagtggcagcctttcgtggaagattaaaatgcagtgtgatcaagattg-acaagcaatctgctt-ttgcagATTTGATCGCGACTGGAAAAAGATTGAAGCTTTCGTTGGTTCTAAGACAGTCATACAG
|| | || || || | | || | | || || | || | |||| || | | || || || || |||||| | |||||||| |||||||||||||| ||||||| |||||||| || |||
gtgatgcgtacaatcttaggcaaggattagacacatgcta---tatccaggttgtttggtggtggatctgatatctcttatgtttgtgttttgattattttagGTTTGATAGAGACTGGAAGAAGATTGAAGCTTTTATTGGTTCAAAGACAGTGATTCAG
upper sequence: PP1S160_6V6.1 (Physcomitrella patens), 3'ss of exon 2
lower sequence: Vv08s0040g03220.t01 (Vitis vinifera), 3'ss of exon 1
---tggagtaggaaaactggattttagaatgcttaagtggcagcctttcgtggaagattaaaatgcagtgtgatcaagattgacaagcaatctgcttttgcagATTTGATCGCGACTGGAAAAAGATTGAAGCTTTCGTTGGTTCTAAGACAGTCATACAG
|| | ||| | ||| | | | | | || || | || || | | || | || | | | |||| ||||||||| || ||||||||||| ||||||| ||| |||||||| |||||||| || |||
cagccttgtttgccgtctgtactttctgaaaaaagacatgggacttctcatgaa---ttttcttgttttttactctaatctgcctcttatatggatttttcagATTTGACCGTGACTGGAAAAAAATTGAAGATTTTGTTGGTTCAAAGACAGTGATTCAG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.cgtggaagattaaaatgcagtgtgatcaagattgacaagcaatctgcttttgcagATTTGATCGCGACTGGAAAAAGATTGAAGCTTTCGTTGGTTCTAAGACAGTCATACAG
gattgac putative branch site (score: 3)
tctgctttt putative PPT
aagattaaaat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
tggagtaggaaaactggattttagaatgcttaagtggcagcctttcgtggaagattaaaatgcagtgtgatcaagattgacaagcaatctgcttttgcagATTTGATCGCGACTGGAAAAAGATTGAAGCTTTCGTTGGTTCTAAGACAGTCATACAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGC