Sequence
atgc intronic sequence ATGC exonic sequencegtcagtggtgaccagcttggtgatgagttcaagggatacgttttcaagattatgggaggatgtgacaagcagggtttccccatgaagCAGGGTGTCTTGACCCAGGGACGTGTGCAACTGCTGATGCACCGAG
Basic information
species | Physcomitrella patens |
transcript | PP1S311_33V6.2 |
intron # | 3 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: PP1S311_33V6.2 (Physcomitrella patens), 3'ss of exon 3
lower sequence: LOC_Os03g27260.1 (Oryza sativa), 3'ss of exon 3
--------------------------------------------------------------gtcagtggtgaccagcttggtgatgagttcaagggatacgttttcaagattatgggaggatgtgacaagcagggtttccccatgaagCAGGGTGTCTTGACCCAGGGACGTGTGCAACTGCTGATGCACCGAG
| | | | | | ||| | || |||||||| || || |||||||| |||||||| ||||||||||| ||||||||||||||||||||||| | || |||||||| | || ||
gtaatttctttggcaatttgctccatgattcttcaactgtcttgctatttaatgagttggatgactaagtttgtctgtttgtacagGAATTCAAGGGCTATGTATTCAAGATCATGGGAGGCTGTGACAAGCAAGGTTTCCCCATGAAGCAGGGTGTGCTTACTTCTGGACGTGTCCGCCTTCTCC---------
upper sequence: PP1S311_33V6.2 (Physcomitrella patens), 3'ss of exon 3
lower sequence: LOC_Os07g42950.1 (Oryza sativa), 3'ss of exon 3
----------------------------------------------------------gtcagtggtgaccagcttggtgatgagttcaagggatacgttttcaagattatgggaggatgtgacaagcagggtttccccatgaagCAGGGTGTCTTGACCCAGGGACGTGTGCAACTGCTGATGCACCGAG
| | || | | || |||||||| || || |||||||| ||||| || |||||||||||||||||||| ||||||||||| || | || |||||||| | || ||
gtaatatcgtgaggcctctgatgtttcctaattactgttacctagtcttaagatgttaacatatctctctcctttttctcagGAATTCAAGGGCTATGTCTTCAAGATCATGGGGGGTTGTGACAAGCAGGGTTTCCCTATGAAGCAGGGAGTGCTCACTGCTGGACGTGTCCGCCTTCTTC---------
upper sequence: PP1S311_33V6.2 (Physcomitrella patens), 3'ss of exon 3
lower sequence: GRMZM2G054136_T09 (Zea mays), 3'ss of exon 3
-----------------------------------------------------------------gtca-gtggtgaccagcttggtgatgagttcaagggatacgttttcaagattatgggaggatgtgacaagcagggtttccccatgaagCAGGGTGTCTTGACCCAGGGACGTGTGCAACTGCTGATGCACCGAG
|| | || | | || | ||||||||||| || || |||||||| ||||| |||||||||||||| || ||||| |||||||| || || ||||| || ||||| | || |||
gtaaactttgggatgacttatttcttgatccatgactcttgctgatttcatacttaaatataggtgtgatatgtttctttgttttgcag-
upper sequence: PP1S311_33V6.2 (Physcomitrella patens), 3'ss of exon 3
lower sequence: GRMZM2G054136_T08 (Zea mays), 3'ss of exon 3
-------------------------------------------------------------------------------------------gtca-gtggtgaccagcttggtgatgagttcaagggatacgttttcaagattatgggaggatgtgacaagcagggtttccccatgaagCAGGGTGTCTTGACCCAGGGACGTGTGCAACTGCTGATGCACCGAG
|| | || | | || | ||||||||||| || || |||||||| ||||| |||||||||||||| || ||||| |||||||| || || ||||| || ||||| | || |||
gtcagtggtgatgctctgggtgaggtaaactttggggtgacttatttcttgatccatgactcttgctgatttcatacttaaaaatataggtgtgatatgtttctttgttttgcag-
upper sequence: PP1S311_33V6.2 (Physcomitrella patens), 3'ss of exon 3
lower sequence: GRMZM2G054136_T05 (Zea mays), 3'ss of exon 3
----------------------------------------------------------------------------gtca-gtggtgaccagcttggtgatgagttcaagggatacgttttcaagattatgggaggatgtgacaagcagggtttccccatgaagCAGGGTGTCTTGACCCAGGGACGTGTGCAACTGCTGATGCACCGAG
|| | || | | || | ||||||||||| || || |||||||| ||||| |||||||||||||| || ||||| |||||||| || || ||||| || ||||| | || |||
ctgggtgaggtaaactttggggtgacttatttcttgatccatgactcttgctgatttcatacttaaaaatataggtgtgatatgtttctttgttttgcag-
upper sequence: PP1S311_33V6.2 (Physcomitrella patens), 3'ss of exon 3
lower sequence: GRMZM2G040600_T01 (Zea mays), 3'ss of exon 5
----------------------------------------------------------------------------gtca-gtggtgaccagcttggtgatgagttcaagggatacgttttcaagattatgggaggatgtgacaagcagggtttccccatgaagCAGGGTGTCTTGACCCAGGGACGTGTGCAACTGCTGATGCACCGAG
|| | || | | || | ||||||||||| || || |||||||| ||||| |||||||||||||| || ||||| |||||||| || || ||||| || ||||| | || |||
gagttgaatttacaaactttgggatgacttatttcttgatccatgactcttgctgatgtcatacttaaatataggtgtgatatgttcctttgttttgcag-
upper sequence: PP1S311_33V6.2 (Physcomitrella patens), 3'ss of exon 3
lower sequence: GRMZM2G054136_T01 (Zea mays), 3'ss of exon 3
-------------------------------------------------------------------gtca-gtggtgaccagcttggtgatgagttcaagggatacgttttcaagattatgggaggatgtgacaagcagggtttccccatgaagCAGGGTGTCTTGACCCAGGGACGTGTGCAACTGCTGATGCACCGAG
|| | || | | || | ||||||||||| || || |||||||| ||||| |||||||||||||| || ||||| |||||||| || || ||||| || ||||| | || |||
gtaaactttggggtgacttatttcttgatccatgactcttgctgatttcatacttaaaaatataggtgtgatatgtttctttgttttgcag-
upper sequence: PP1S311_33V6.2 (Physcomitrella patens), 3'ss of exon 3
lower sequence: GRMZM5G851698_T02 (Zea mays), 3'ss of exon 3
------------------------------------------------------------------gtcagtggtgaccagcttggtgatgagttcaagggatacgttttcaagattatgggaggatgtgacaagcagggtttccccatgaagCAGGGTGTCTTGACCCAGGGACGTGTGCAACTGCTGATGCACCGAG
|| | ||| || | ||||| ||||| || || |||||||| ||||| ||||||||||| || || ||||| |||||||| || || |||| || ||||| | || |||
gtaaattttctgctttcttatttcttgatccatgccccctattgctgatttcatacttaattataggtgtgatgtgtttcttttttgcagGAGTTTAAGGGTTATGTCTTCAAGATCATGGGTGGATGTGACAAACAAGGCTTCCCAATGAAGCAAGGAGTTCTGACTTCTGGTCGTGTCCGCCTTCTGC---------
upper sequence: PP1S311_33V6.2 (Physcomitrella patens), 3'ss of exon 3
lower sequence: AT5G10360.1 (Arabidopsis thaliana), 3'ss of exon 3
-----------------------------------------------------------------------gtcagtggtgaccagcttggtgatgagttcaagggatacgttttcaagattatgggaggatgtgacaagcagggtttccccatgaagCAGGGTGTCTTGACCCAGGGACGTGTGCAACTGCTGATGCACCGAG
|| || ||| | ||| | || |||||||||||||| |||||||| |||||||||||||||||||| |||||||| ||||| || || || | || | || ||||| | || ||
gtgaaattttttctcctggttcagtgtttttttctgatgtcttgtgagttcagtatacttaacagaattgtgtgtgttttgagctatttgcag-
upper sequence: PP1S311_33V6.2 (Physcomitrella patens), 3'ss of exon 3
lower sequence: AT4G31700.2 (Arabidopsis thaliana), 3'ss of exon 1
-------------------------------------------------------------------------gtcagtggtgaccagct--tggtg-atgagttcaagggatacgttttcaagattatgggaggatgtgacaagcagggtttccccatgaagCAGGGTGTCTTGACCCAGGGACGTGTGCAACTGCTGATGCACCGAG
| | ||| | | | || | |||||||| ||||||||||||||||| | ||| || || || ||||| |||||||| ||||||||||| || ||||| | || ||||| | || ||
aggtacagattccatttttcttactttgatctaatgagtgtgaagattagcatttcgaagcagatgatgatgttttgtttatgaattgttgttattgcagGAGTTCAAAGGATACGTTTTCAAGATCAAGGGTGGTTGCGATAAGCAAGGTTTCCCAATGAAGCAGGGAGTTTTGACTCCAGGCCGTGTTCGCCTTTTGC---------
upper sequence: PP1S311_33V6.2 (Physcomitrella patens), 3'ss of exon 3
lower sequence: AT4G31700.1 (Arabidopsis thaliana), 3'ss of exon 3
-----------------------------------------------------------------------gtcagtggtgaccagc--ttggtg-atgagttcaagggatacgttttcaagattatgggaggatgtgacaagcagggtttccccatgaagCAGGGTGTCTTGACCCAGGGACGTGTGCAACTGCTGATGCACCGAG
| | ||| | || || | |||||||| ||||||||||||||||| | ||| || || || ||||| |||||||| ||||||||||| || ||||| | || ||||| | || ||
gtacagattccatttttcttactttgatctaatgagtgtgaagattagcatttcgaagcagatgatgatgttttgtttatgaattgttgttattgcagGAGTTCAAAGGATACGTTTTCAAGATCAAGGGTGGTTGCGATAAGCAAGGTTTCCCAATGAAGCAGGGAGTTTTGACTCCAGGCCGTGTTCGCCTTTTGC---------
upper sequence: PP1S311_33V6.2 (Physcomitrella patens), 3'ss of exon 3
lower sequence: Vv03s0017g01350.t01 (Vitis vinifera), 3'ss of exon 3
--------------------------------------------------------------gtcagtggtgaccagcttggtgatgagttcaagggatacgttttcaagattatgggaggatgtgacaagcagggtttccccatgaagCAGGGTGTCTTGACCCAGGGACGTGTGCAACTGCTGATGCACCGAG
| || | | |||| ||||||||||| || ||||||||||| ||||| || ||||||||||| || || |||||||||||||| || |||| | || ||||| || ||
gtatgccttttctgctcttctcccacttatttatctcatattgtttgatctactaatcatacaaaacatgtcatctgcttcacag-
upper sequence: PP1S311_33V6.2 (Physcomitrella patens), 3'ss of exon 3
lower sequence: Vv07s0191g00060.t01 (Vitis vinifera), 3'ss of exon 3
------------------------------------------------------------gtcagtggtgaccagcttggtgatgagttcaagggatacgttttcaagattatgggaggatgtgacaagcagggtttccccatgaagCAGGGTGTCTTGACCCAGGGACGTGTGCAACTGCTGATGCACCGAG
| | | | | || | | ||||||||||| || || ||||| || |||||||| ||||||||||| ||||| || ||||||||||| || |||||| || || || ||||| |||
gtatgattttgttactattcttcttaggataacttgccctttgttaggaatgatttattgatgtatcttaagcgtgtttgacagGAGTTCAAGGGTTATGTATTCAAAATAATGGGAGGCTGTGACAAGCAAGGTTTTCCAATGAAGCAGGGAGTACTGACCCCAGGCCGAGTCCAACTTCTGC---------
upper sequence: PP1S311_33V6.2 (Physcomitrella patens), 3'ss of exon 3
lower sequence: Vv18s0001g06290.t01 (Vitis vinifera), 3'ss of exon 3
-----------------------------------------------------------------gtcagtggtgaccagcttg-gtgat--gagttcaagggatacgttttcaagattatgggaggatgtgacaagcagggtttccccatgaagCAGGGTGTCTTGACCCAGGGACGTGTGCAACTGCTGATGCACCGAG
| || | | ||| |||| || || || || || || ||||| || |||||||| ||||||||||| || ||||| ||||||||||| || || || | || ||||| || ||
gtaagcatttaccattgttatgcaatgccaaaattctactatcagactagatttatataacatttatttttgtttgtttgtttgtgtgacagGAATTTAATGGCTATGTATTCAAAATCATGGGAGGCTGTGACAAGCAAGGGTTCCCAATGAAGCAGGGAGTGTTAACTCCTGGTCGTGTTAGTCTCTTGC---------
upper sequence: PP1S311_33V6.2 (Physcomitrella patens), 3'ss of exon 3
lower sequence: EDP01810 (Chlamydomonas reinhardtii), 3'ss of exon 1
--------------------------------------------------------------------------------------------gtcagtggtgaccagctt--ggtgatgagttca-agggatacgttttcaagattatgggaggatgtgacaagcagggtttccccatgaagCAGGGTGTCTTGACCCAGGGACGTGTGCAACTGCTGATGCACCGAG
| | || || | |||| | | | | | | |||| |||||| | ||||| || || ||||||||||| ||| ||||||||||||||||| ||||| | | || |||| ||||||||| || |
gtgcgtttgctgcggaacagctggtgccaaaaattgtctgtgttcgcggggctgggcggccgccggccgcccgcacctcactggagcggccacttactgctgggctgcttccgccgttccgctgacagGGCTACGTTCTGAAGATCGCTGGTGGCCAGGACAAGCAGGGCTTCGCCATGAAGCAGGGTGTCCTGACCAATGCCCGCGTGCGTCTGCTGATGACCCCCG
upper sequence: PP1S311_33V6.2 (Physcomitrella patens), 3'ss of exon 3
lower sequence: EFJ14726 (Selaginella moellendorffii), 3'ss of exon 2
----------------------------gtcagtggtgaccagcttggtg-atgagttcaagggatacgttttcaagattatgggaggatgtgacaagcagggtttccccatgaagCAGGGTGTCTTGACCCAGGGACGTGTGCAACTGCTGATGCACCGAG
|| || | | ||| | || ||||| || || || |||||||| |||||||||||||||||| | || ||||| ||||||||||| ||| | | | ||||||| || |||
gtgaattcgtcggcatttgagctttgctgtttgttctaagatttgcagtgcagGAATTCAAAGGCTATGTCTTCAAGATCATGGGAGGATGTGACAAGGATGGCTTCCCTATGAAGCAGGGCGTCCTCAAGACGAAGCGTGTGCGCCTCCTGT---------
upper sequence: PP1S311_33V6.2 (Physcomitrella patens), 3'ss of exon 3
lower sequence: EFJ26393 (Selaginella moellendorffii), 3'ss of exon 2
----------------------------gtcagtggtgaccagcttggtg-atgagttcaagggatacgttttcaagattatgggaggatgtgacaagcagggtttccccatgaagCAGGGTGTCTTGACCCAGGGACGTGTGCAACTGCTGATGCACCGAG
|| || | | ||| | || ||||| || || || |||||||| |||||||||||||||||| | || ||||| ||||||||||| || | | | ||||||| || |||
gtgaattcgtcggcatttgagctttgctgtttgttctaagatttgcagtgcagGAATTCAAAGGCTATGTCTTCAAGATCATGGGAGGATGTGACAAGGATGGCTTCCCTATGAAGCAGGGCGTTCTCAAGACGAAGCGTGTGCGCCTCCTGT--------- atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.gggatacgttttcaagattatgggaggatgtgacaagcagggtttccccatgaagCAGGGTGTCTTGACCCAGGGACGTGTGCAACTGCTGATGCACCGAG
tttccccat CT-rich tract
aagattat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtcagtggtgaccagcttggtgatgagttcaagggatacgttttcaagattatgggaggatgtgacaagcagggtttccccatgaagCAGGGTGTCTTGACCCAGGGACGTGTGCAACTGCTGATGCACCGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGAT