Sequence
atgc intronic sequence ATGC exonic sequence...acatctgttagctttggcaaggactttggtcgattcgcctttttcatgtgtgaatttcaagacgagattgttgccgacgtggtatgcttcttgcatgcagGTGTATACAGTGGGGCCAGAATATGCTCATGCAGAAGCTAGAAAGTCTCCTGTTGTGGATGGTGTAGTAATGAGAAGTGCTGATGGAAAGGAG
Basic information
species | Physcomitrella patens |
transcript | PP1S112_67V6.1 |
intron # | 8 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: PP1S112_67V6.1 (Physcomitrella patens), 3'ss of exon 8
lower sequence: GLYMA19G02260.1 (Glycine max), 3'ss of exon 6
--------------------acatctgttagctttggcaaggactttggtcgattcgcctttttcatgtgtgaatttcaagacg--agattgttgccgacgtggtatgcttcttgcatgcagGTGTATACAGTGGGGCCAGAATATGCTCATGCAGAAGCTAGAAAGTCTCCTGTTGTGGATGGTGTAGTAATGAGAAGTGCTGATGGAAAGGAG
| | || || ||| | ||| | | || | | || | | ||| || | | | | | | || || ||||||||||||| || || |||||||| ||||| || || || |||||||||||||| |||||||| || ||||||| | || |||| |||||
gtttggcagttttgagatttatgttgctttctattccttttctcttaaatgtatttggaatgtttctccatatcctttagcatattagaatggtctcctagaattttcataaatgactgtagGTGTATACAGTAGGTCCTGAATATGCGCATGCTGAGGCAAGGAAGTCTCCTGTTGTTGATGGTGTTGTTATGAGAAATCCTAATGGGAAGGAA
upper sequence: PP1S112_67V6.1 (Physcomitrella patens), 3'ss of exon 8
lower sequence: GLYMA13G05060.1 (Glycine max), 3'ss of exon 8
----acatctgttagctttggcaaggactttggtcgattcgcctttttcatgtgt---gaatttcaagacgagattgttgccgacgtggtatg------------cttcttgcatg---cagGTGTATACAGTGGGGCCAGAATATGCTCATGCAGAAGCTAGAAAGTCTCCTGTTGTGGATGGTGTAGTAATGAGAAGTGCTGATGGAAAGGAG
| | || || || | || | || || || |||| | |||| | | || | | | ||| ||| | ||| ||||||||||||| || || |||||||| ||||| || || || |||||||||||||| |||||||| || ||||||| | |||||| |||||
gtttggctgttttgagatttataatgctttctatttttttttctcttaaatgtatttggaatgtttgtccatatcctttagcatattagaatggtctcttagaattttcataaatgacttagGTGTATACAGTAGGTCCTGAATATGCGCATGCTGAGGCAAGGAAGTCTCCTGTTGTTGATGGTGTTGTTATGAGAAATCTTGATGGGAAGGAA
upper sequence: PP1S112_67V6.1 (Physcomitrella patens), 3'ss of exon 8
lower sequence: GLYMA09G37610.1 (Glycine max), 3'ss of exon 6
----------------------------------------------------acatctgttagctttggcaaggactttggtcgattcgcct--ttttcatgtgtgaattt-caagac-gagattgttgccgacgtggtatgcttcttgcatgcagGTGTATACAGTGGGGCCAGAATATGCTCATGCAGAAGCTAGAAAGTCTCCTGTTGTGGATGGTGTAGTAATGAGAAGTGCTGATGGAAAGGAG
| ||| | | ||| ||| || | | | || | | ||| || || || ||| || | || | | || || |||| |||||||| || || |||||||||||||| || || || ||||||||||| || |||||||| || ||||||| | ||||||| |||||
gtttggctgtgaagtttatgttgctttgtgtttgttttattgtttctttatttttttaattatatatatttgggattttttcagacttatgtgatgtttctaaatagtttttcacaacagaaattattttcaacat--ttcaacatatgattgtagGTATATACAGTTGGCCCTGAATATGCTCATGCTGAGGCAAGGAAGTCTCCTGTGGTTGATGGTGTTGTGATGAGAAATACTGATGGGAAGGAA
upper sequence: PP1S112_67V6.1 (Physcomitrella patens), 3'ss of exon 8
lower sequence: GLYMA18G49000.1 (Glycine max), 3'ss of exon 8
-------------------------------------------------------acatctgttagctttggcaaggacttt---ggtcgattcgcctttttcatgtgtgaatttcaagacgagattgttgccgacgtggtatgcttcttgcatgcagGTGTATACAGTGGGGCCAGAATATGCTCATGCAGAAGCTAGAAAGTCTCCTGTTGTGGATGGTGTAGTAATGAGAAGTGCTGATGGAAAGGAG
| | | || ||| ||| | || | ||| | | | ||||| | | | | | | || || || |||| |||||||| || || |||||||||||||| || || || ||||||||||| || |||||||| || ||||||| | ||||||| |||||
gtttgactatgaagtttatgttgctttgtgtttattttattgtttctttatttttttaattatatatttgggcttttttttttcagacacatgtgatgtttctacata-gtttttcacaatagaaattcttttcaaacattttgacatatgattgtagGTATATACAGTTGGCCCTGAATATGCTCATGCTGAGGCAAGGAAGTCTCCTGTGGTTGATGGTGTTGTGATGAGAAATCCTGATGGGAAGGAA
upper sequence: PP1S112_67V6.1 (Physcomitrella patens), 3'ss of exon 8
lower sequence: AT3G01310.2 (Arabidopsis thaliana), 3'ss of exon 9
acatctgttagctttggcaaggactttggtcgattcgcctttttcatgtgtgaatttcaag---acgagattgttgccgacgtggtatgcttcttgcatgcagGTGTATACAGTGGGGCCAGAATATGCTCATGCAGAAGCTAGAAAGTCTCCTGTTGTGGATGGTGTAGTAATGAGAAGTGCTGATGGAAAGGAG
| | ||||| || || || | || | | | ||| | | | | | ||| | | ||| | | | | | | ||||| ||||||||||| || ||||| || ||||| ||||| |||||||| |||||||| |||||||| || ||||| | | | ||||| |||||
atgctgcatggctttc-cacctgctgatgtagcttttattgctgcttgtttctgtctggtgagcatgagttctcaactgaca--atcttcctggtaaacacagGTCTATACAGTGGGTCCTGAATACGCACATGCTGAAGCAAGAAAGTCACCTGTTGTTGATGGTGTTGTTATGAGGAATACAGATGGGAAGGAA
upper sequence: PP1S112_67V6.1 (Physcomitrella patens), 3'ss of exon 8
lower sequence: AT5G15070.1 (Arabidopsis thaliana), 3'ss of exon 9
acatctgttagct-ttggcaaggactttggtcgattcgcctttttcatgtgtgaatttcaa----gacgagattgttgccgacgtggtatgcttcttgcatgcagGTGTATACAGTGGGGCCAGAATATGCTCATGCAGAAGCTAGAAAGTCTCCTGTTGTGGATGGTGTAGTAATGAGAAGTGCTGATGGAAAGGAG
|| ||| | | || ||| | | | | | | || |||| | |||||| || | | ||| || | | || || ||||| || || ||||| || |||||||| || || ||||| ||||| || |||||||| ||||||||||||||||||| | | ||||| |||||
--gtcgtaaggctatctggaatagttttttttttctggattatgttttggttgaagcttggctttgacgagtttttgactgaca--gtctacc-ctgaaatacagGTCTACACTGTGGGTCCCGAATATGCACACGCTGAAGCAAGAAAATCACCTGTTGTTGATGGTGTAGTAATGAGAAATCCAGATGGGAAGGAA
upper sequence: PP1S112_67V6.1 (Physcomitrella patens), 3'ss of exon 8
lower sequence: Vv14s0066g02540.t01 (Vitis vinifera), 3'ss of exon 8
acatctgttagctttggcaaggactttggtcgattcgcctttttcatgtgtgaatttcaagacgagattgttgccgacgtggtatgcttcttgc------atg-cagGTGTATACAGTGGGGCCAGAATATGCTCATGCAGAAGCTAGAAAGTCTCCTGTTGTGGATGGTGTAGTAATGAGAAGTGCTGATGGAAAGGAG
|| | | || ||| | | |||| | | | ||||||| | | | ||| | || | | | |||||||| || ||||||||||||| || || |||||||| ||||| || || || |||||||||||||| ||||| || || ||||||| | ||||| || ||
--atgtaatgcctatggta-gtcttttgccttttccatcattttcatttttcactttttattt----ttatcatcagttgatcaagcttcttgtcaatttataatagGTGTATACAGTTGGCCCTGAATATGCACATGCTGAGGCAAGGAAGTCTCCTGTTGTTGATGGCGTTGTTATGAGAAACCCCGATGGGAAAGAA atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.atgtgtgaatttcaagacgagattgttgccgacgtggtatgcttcttgcatgcagGTGTATACAGTGGGGCCAGAATATGCTCATGCAGAAGCTAGAAAGTCTCCTGTTGTGGATGGTGTAGTAATGAGAAGTGCTGATGGAAAGGAG
tgcttctt CT-rich tract
aatttcaa 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
acatctgttagctttggcaaggactttggtcgattcgcctttttcatgtgtgaatttcaagacgagattgttgccgacgtggtatgcttcttgcatgcagGTGTATACAGTGGGGCCAGAATATGCTCATGCAGAAGCTAGAAAGTCTCCTGTTGTGGATGGTGTAGTAATGAGAAGTGCTGATGGAAAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAG