Sequence
atgc intronic sequence ATGC exonic sequencegttagtgtcaagcactcaatctggcatttcatgatgtcaggccacagcttgccgtttaatgcaatgtgcggctgcaatccacagatgaggaaccttgaaagattctcctgtaatgccagatttccttaagcgcaaacgtttcattcttcctgtcatggactcgtgattgtgatgcagTTGGTAAAAAATCCGGGACTCTTCGATGTCTTGGTGATGCCTAATTTATATGGAGACATTATCAGTGATCTCTGTGCTGGTCTGATTGGAGGGTTGGGTT
Basic information
species | Physcomitrella patens |
transcript | PP1S78_143V6.1 |
intron # | 4 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: PP1S78_143V6.1 (Physcomitrella patens), 3'ss of exon 4
lower sequence: LOC_Os01g16900.3 (Oryza sativa), 3'ss of exon 6
----gttagtgt-caagcactcaatctggcatttca--tgatgtcag-gccacagcttgccgtttaatgcaatgtgcggctgcaatccacagatgaggaaccttgaaagattctcctgtaatgccag--atttccttaagcgc---aaacgtttcattcttcctgtcatggactcgtgattgtgat------gcagTTGGTAAAAAATCCGGGACTCTTCGATGTCTTGGTGATGCCTAATTTATATGGAGACATTATCAGTGATCTCTGTGCTGGTCTGATTGGAGGGTTGGGTT
||| | | | || || | | || || ||| | | ||| | | | || || || ||| || |||| || || || || | || | || | ||| | | || || ||| | ||| || | |||| | | |||| | || || ||||| || || || ||||| |||||||||| ||| | ||||| || ||||| |||||||| |||||||||||||||||||| ||||| |
gtatgttgttctgctgataccaaaacctgtgctttgtttggtgttaatgttgaagcattcttcacactggtctgatgatctctgatcgacc--tgagaaatgc-aaattatcctatttgtattctagccacttctattgctgtcctggacagttaattaatgacaccattgatttgtgaacattgtccccttgcagCTTGTGAAGAATCCTGGTCTTTTTGATGTACTGGTGATGCCAAATCTTTATGGTGATATTATTAGTGATCTTTGTGCTGGTCTGATTGGAGGCTTGGGCT
upper sequence: PP1S78_143V6.1 (Physcomitrella patens), 3'ss of exon 4
lower sequence: AT3G09810.1 (Arabidopsis thaliana), 3'ss of exon 4
-------gtta-gtgtcaagcactcaatctggcatttca--tgatgtcaggccacagcttgccgtt---taatgcaatgtgcggctgcaatccacagatgaggaaccttgaaagattctcctgtaa----tgccagatttccttaagcgcaaacgtttcat-tcttcctgtcatggactcgtgattgtgat----gcagTTGGTAAAAAATCCGGGACTCTTCGATGTCTTGGTGATGCCTAATTTATATGGAGACATTATCAGTGATCTCTGTGCTGGTCTGATTGGAGGGTTGGGTT
| | || | ||| | |||| || || | |||| | | | || ||| ||| | | | || | ||| ||| || ||||| || | || | | | | | ||| || || | | | | | ||| | | || | || ||| | || ||||| || | ||| || ||||||||||||||||| ||| | |||||||| |||||||| ||| | |||||||| || |||| || | ||
gtaagctataacatgatatccaccctatcttttgttccaaattatgtaaaggtcaatctcattgttaattaagttagtatttgggataatcttgttgattttgaaggtt---agatttcccagcaacccatacttgggtctgcttttcgctaattttacttatggaacaatgtgggattgataatcttaattctgacagCTTGTGAAAAACCCAGCACTTTTTGATGTCTTGGTGATGCCAAATCTCTATGGAGATATTATCAGCGATTTGTGTGCTGGACTTGTTGGGGGACTAGGAC
upper sequence: PP1S78_143V6.1 (Physcomitrella patens), 3'ss of exon 4
lower sequence: Vv08s0040g01700.t01 (Vitis vinifera), 3'ss of exon 4
gttagtgtcaagcactcaatctggcatttcatgatgtcaggccacagcttgccgtttaatgcaatgtgcggctgcaatccacagatgaggaaccttgaaagattct---cctgtaatgccagatttccttaagcgcaaacgtttcattcttcctgtcatggactcgtgattgtgatgcagTTGGTAAAAAATCCGGGACTCTTCGATGTCTTGGTGATGCCTAATTTATATGGAGACATTATCAGTGATCTCTGTGCTGGTCTGATTGGAGGGTTGGGTT
|||| | | || ||| | ||||| | | | || | | | | || | |||| | | | || | | ||| ||| | | ||| | || || ||||| | || || ||||| |||||||||||||| | ||||| |||||||| ||||||||||||||||| ||||||| || | || |
-------------------------------------------------------------------------gcaaaatatgtaagaaaaacg--agatcattctaggcatatgatacagaaatgcactaggataaaac-taggaaccactctaacttct-ctcttgaat---aaacagCTTGTGAAGAATCCTGCGCTTTTTGATGTGTTGGTGATGCCTAACCTCTATGGTGACATTATTAGTGATCTCTGTGCTGGCTTGATTGGGGGACTAGGCT
upper sequence: PP1S78_143V6.1 (Physcomitrella patens), 3'ss of exon 4
lower sequence: EFJ18109 (Selaginella moellendorffii), 3'ss of exon 5
gttagtgtcaagcactcaatctggcatttcatgatgtcaggccacagcttgccgtttaatgcaatgtgcggctgcaatccacagatgaggaaccttgaaagattctcctgtaatgccagatttccttaagcgcaaacgtttcattcttcctgtcatggactcgtgattgtga--tgcagTTGGTAAAAAATCCGGGACTCTTCGATGTCTTGGTGATGCCTAATTTATATGGAGACATTATCAGTGATCTCTGTGCTGGTCTGATTGGAGGGTTGGGTT
| | | || || || ||| | ||| | || || |||| ||||| | ||||||||||| | | || || || ||||||||||| || || |||||||| || |||||||||||||| |||||||| || || || | || |
----------------------------------------------------------------------------------------------------------------------gtaagcttcaaaatcagactttttgtcgttcagtctctctgatcctgcttgtttcttgcagCTCGTAAAAAATCCTGCCTTGTTTGACGTGTTGGTGATGCCAAACTTGTATGGAGATATCATCAGTGATCTCTGCGCTGGTCTCATAGGCGGCCTTGGAT
upper sequence: PP1S78_143V6.1 (Physcomitrella patens), 3'ss of exon 4
lower sequence: EFJ09610 (Selaginella moellendorffii), 3'ss of exon 4
gttagtgtcaagcactcaatctggcatttcatgatgtcaggccacagcttgccgtttaatgcaatgtgcggctgcaatccacagatgaggaaccttgaaagattctcctgtaatgccagatttccttaagcgcaaacgtttcattcttcctgtcatggactcgtgattgtga--tgcagTTGGTAAAAAATCCGGGACTCTTCGATGTCTTGGTGATGCCTAATTTATATGGAGACATTATCAGTGATCTCTGTGCTGGTCTGATTGGAGGGTTGGGTT
| | | || || || ||| | ||| | || || |||| ||||| | ||||||||||| | | || || || ||||||||||| || || |||||||| || |||||||||||||| |||||||| || || || | || |
----------------------------------------------------------------------------------------------------------------------gtaagcttcaaaatcagactttttgtcgttcagcctctctgatcctgcttgtttcttgcagCTCGTAAAAAATCCTGCCTTGTTTGACGTGTTGGTGATGCCAAACTTGTATGGAGATATCATCAGTGATCTCTGCGCTGGTCTCATAGGCGGCCTTGGAT atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tccttaagcgcaaacgtttcattcttcctgtcatggactcgtgattgtgatgcagTTGGTAAAAAATCCGGGACTCTTCGATGTCTTGGTGATGCCTAATTTATATGGAGACATTATCAGTGATCTCTGTGCTGGTCTGATTGGAGGGTTGGGTT
tttcatt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gttagtgtcaagcactcaatctggcatttcatgatgtcaggccacagcttgccgtttaatgcaatgtgcggctgcaatccacagatgaggaaccttgaaagattctcctgtaatgccagatttccttaagcgcaaacgtttcattcttcctgtcatggactcgtgattgtgatgcagTTGGTAAAAAATCCGGGACTCTTCGATGTCTTGGTGATGCCTAATTTATATGGAGACATTATCAGTGATCTCTGTGCTGGTCTGATTGGAGGGTTGGGTT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGG