Sequence
atgc intronic sequence ATGC exonic sequence...aagttattttaaggagatatcaccatagaaaaacaattaaaataatgacgctgcttgtcttctagaagttctaaccaactgtcaagtgcactctacacagGAGATGGAGAAACAGTACCTGCAAAAACTCTGCGGTCTAAACCTAAAGCAAATTAACAACTGGTTCATCAATGAGCGCAAGCGGCACTGGAGCTGCGAGG
Basic information
species | Physcomitrella patens |
transcript | PP1S235_27V6.1 |
intron # | 6 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: PP1S235_27V6.1 (Physcomitrella patens), 3'ss of exon 6
lower sequence: GRMZM2G017087_T03 (Zea mays), 3'ss of exon 3
aagttattttaaggagatatcaccata-gaaaaacaattaaaataatgacgctgcttgtcttctagaagt--tctaaccaactgtcaagtgcactctacacagGAGATGGAGAAA-CAGTACCTGCAAAAACTCTGCGGTCTAAACCTAAAGCAAATTAACAACTGGTTCATCAATGAGCGCAAGCGGCACTGGA-GCTGCGAGG
|||| || || | | | | ||| | | ||||| || || || | ||||||||| | | | ||||||| |||| | || || | || ||| || |||| ||||| || ||||||||||||||||| |||| ||||||||||||| || |
-ttttatcatatcttcattttgttggatgttttgtatacggcatatagcctgtgcttccctactggatatgaattaaccaactcttcccatcggt--gagcagGAGACTCAGAAGGTGGCACTGGCTGAGTCTAC-CGGGCTTGACCTGAAGCAGATCAACAACTGGTTCATCAACCAGCGGAAGCGGCACTGGAAGCCATCCG-
upper sequence: PP1S235_27V6.1 (Physcomitrella patens), 3'ss of exon 6
lower sequence: GRMZM2G135447_T01 (Zea mays), 3'ss of exon 4
------------------------------aagttattttaaggagatatcacca--tagaaaaacaattaaaataatgacgctgcttgtcttctagaagttctaaccaactgtcaagtgcactctacacagGAGATGGAGAA-ACAGTACCTGCAAAAACTCTGCGGTCTAAACCTAAAGCAAATTAACAACTGGTTCATCAATGAGCGCAAGCGGCACTGGAGCTGCGAGG
| | | ||| | || | | | || || || | | | | || | | | ||||| | | |||| || ||||||| |||||| | | | ||| | || ||| || ||| ||||| || ||||||||||||||||| |||| ||||||||||||| | |
gtaagaccctacctatgtttccttccatccatgcattgctaatacaacggcaactactgtgtctatgtttggaagaagaaaaaaaatgaagcttttgatgcatga--ctactgtttcgagtactc-ac-cagGAGACGGAGAAGATGGCGCTCGCAGAGACGAC-CGGGCTGGACCCGAAGCAGATCAACAACTGGTTCATCAACCAGCGGAAGCGGCACTGGAAGCCGGCGT
upper sequence: PP1S235_27V6.1 (Physcomitrella patens), 3'ss of exon 6
lower sequence: GRMZM2G094241_T01 (Zea mays), 3'ss of exon 4
aagttattttaaggagatat-caccatagaaaaacaattaaaataatgacgctgcttgtcttctagaagttctaaccaactgtcaagtgcactctacacagGAGATGGAGAAACAGTACCTGCAAAAACTCTGCGGTCTAAACCTAAAGCAAATTAACAACTGGTTCATCAATGAGCGCAAGCGGCACTGGA-GCTGCGAGG
||| | || || | | | ||| | | |||| || | | | | |||| | | || | | | || | | | | || ||| || || ||| ||||| || ||||||||||||||||| |||| ||||||||||||| || | |
--------gtaaccatgcatgcatcctggcaaacacgcagcagcagcatcgctcgctggaatggcagatctgtgaccagcattagccggcggtgcagGAGGAGGACAAGGTGAGGCTGGCGGCGGCGACT----GGGCTGGACCCGAAGCAGATCAACAACTGGTTCATCAACCAGCGGAAGCGGCACTGGAAGCCGTCCG-
upper sequence: PP1S235_27V6.1 (Physcomitrella patens), 3'ss of exon 6
lower sequence: GRMZM2G452178_T01 (Zea mays), 3'ss of exon 4
------------------aagttattttaaggagatatcaccatagaaaaacaattaaaataatgacgctgcttgtct---tctagaagttctaaccaactgt-caagtgcac-tct----acacagGAGATGGAGAA-ACAGTACCTGCAAAAACTCTGCGGTCTAAACCTAAAGCAAATTAACAACTGGTTCATCAATGAGCGCAAGCGGCACTGGA-GCTGCGAGG
| | | | | | | | | |||| || | | | || | || | | | |||| | ||| ||| | ||||||| |||||| | | | ||| | | || || ||| ||||| || ||||||||||||||||| |||| ||||||||||||| || | |
gtgagagactaatctcccgtgcggccgtgccttaacacaatgctgacagatcgattaccgtactcatacagcacgcgcgtgccttgtgcccttggctcgctgtgcttgtgtttgtctgaacatgcagGAGACGGAGAAGATCGCGCTGGCAGAGGCGAC-TGGCCTGGACCAGAAGCAGATCAACAACTGGTTCATCAACCAGCGGAAGCGGCACTGGAAGCCGTCGG-
upper sequence: PP1S235_27V6.1 (Physcomitrella patens), 3'ss of exon 6
lower sequence: GLYMA17G01370.1 (Glycine max), 3'ss of exon 4
aagttattttaaggagatatcaccatagaaaaacaattaaaataatgacgctgcttg-----tcttctagaagttctaaccaactgtcaagtgcactctacacagGAGATGGAGAAAC-AGTACCTGCAAAAACTCTGCGGTCTAAACCTAAAGCAAATTAACAACTGGTTCATCAATGAGCGCAAGCGGCACTGGA-GCTGCGAGG
| |||| || | | | | | || || | || || | | | | | || ||| | | || | | | |||| | |||||| |||| | || | |||| | | || || | | |||||||||||||||||||| |||||| | | ||||||||||||| || ||
atattataatagcaataatttttcggtatataagaaacatgttatggaagtttttaggggaacaatttacaaggttttacatgatttta--tgcatta---acagGAATCTCAGAAGCTAGCTCTTGCAGAGTCAACAGGG-CTGGATCAGAAGCAAATTAACAACTGGTTTATCAATCAAAGAAAGCGGCACTGGAAGCCTTCAG- atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tgacgctgcttgtcttctagaagttctaaccaactgtcaagtgcactctacacagGAGATGGAGAAACAGTACCTGCAAAAACTCTGCGGTCTAAACCTAAAGCAAATTAACAACTGGTTCATCAATGAGCGCAAGCGGCACTGGAGCTGCGAGG
ttctaac putative branch site (score: 1)
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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
aagttattttaaggagatatcaccatagaaaaacaattaaaataatgacgctgcttgtcttctagaagttctaaccaactgtcaagtgcactctacacagGAGATGGAGAAACAGTACCTGCAAAAACTCTGCGGTCTAAACCTAAAGCAAATTAACAACTGGTTCATCAATGAGCGCAAGCGGCACTGGAGCTGCGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTGC