Sequence
atgc intronic sequence ATGC exonic sequence...ggttttactcagtatgagacaggtttaaaattatgtgattctgcctctattcaaagaatcacaaaattgtgtcttgatcctgctttgatttctaccatagGTTGAGAATCAGGAAGGTCTGGTGAACTTCGATGACATATTGAAAGAGACAGACGGAGTCATGGTGGCAAGAGGGGACCTGGGAATGGAGATTCCTACGG
Basic information
species | Physcomitrella patens |
transcript | PP1S124_70V6.2 |
intron # | 3 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: PP1S124_70V6.2 (Physcomitrella patens), 3'ss of exon 3
lower sequence: GLYMA02G07800.1 (Glycine max), 3'ss of exon 3
-ggttttactcagtatgagacaggttta--aaattatgtgattctgcctctattcaaagaatcacaaaattgtgtcttgatcctgctttgatttctaccatagGTTGAGAATCAGGAAGGTCTGGTGAACTTCGATGACATATTGAAAGAGACAGACGGAGTCATGGTGGCAAGAGGGGACCTGGGAATGGAGATTCCTACGG
| | || ||| ||| || || ||| || | | | | | |||| | | | ||||||| | | || || | | | |||||||| ||||| || ||| | | || || ||||| ||| || | | |||| | | |||||||||||||||| |||||||||||||| ||||| | |
tgtataagttccctat---acaagtctatgaaaataagaaacagttcttgtattgattaacctcccaaattgtacttatttgttgtcttcttgttttggttagGTTGAAAATCAAGAGGGTGTTGCCAATTTTGATGAAATACTGGCAAATTCAGATGCATTCATGGTGGCAAGAGGTGACCTGGGAATGGAAATTCCAATTG
upper sequence: PP1S124_70V6.2 (Physcomitrella patens), 3'ss of exon 3
lower sequence: GLYMA16G26830.1 (Glycine max), 3'ss of exon 3
----------------------------------------------------------------------ggttttact--cagtatgagacaggtttaaaat---tatgtgattctgcc-------tctattcaaagaatca-caaaattgtgtc-----ttgatcctgc------------tttgatttctaccatagGTTGAGAATCAGGAAGGTCTGGTGAACTTCGATGACATATTGAAAGAGACAGACGGAGTCATGGTGGCAAGAGGGGACCTGGGAATGGAGATTCCTACGG
||||||| || | ||| | ||| ||| | | | || ||||| ||| || | |||| || || | || ||| | |||| | ||| |||||||| ||||| || ||| | | || || ||||| ||| || || | |||| | | |||||||||||||||| |||||||||||||| ||||| | |
gtatccatccttattctcaagtaaatgtattctgttttactttaactcttcaaataatttacagaaatgtcattttactttcactttgattctattttcaaacatacgtataagctctccgtacaagtctatgaaaacaagaaacaaagttctggcattgattaatctcccaaattgtacttatttgttgtctttgttagGTTGAAAATCAAGAGGGTGTTGCAAATTTTGATGAAATACTGGAAAATTCAGATGCATTCATGGTGGCAAGAGGTGACCTGGGAATGGAAATTCCAATTG
upper sequence: PP1S124_70V6.2 (Physcomitrella patens), 3'ss of exon 3
lower sequence: EFJ06845 (Selaginella moellendorffii), 3'ss of exon 2
ggttttactcagtatgagacaggtttaaaattatgtgattctgcctctattcaaagaatcacaaaattgtgtcttgatcctgctttgatttctaccatagGTTGAGAATCAGGAAGGTCTGGTGAACTTCGATGACATATTGAAAGAGACAGACGGAGTCATGGTGGCAAGAGGGGACCTGGGAATGGAGATTCCTACGG
| | | || | | |||| ||| | |||||||||| || ||||| | || ||||||||||||||||||| ||| |||||||| | ||||| || |||| ||||| |||||||| ||||| | |
-------------------------------------------------------gtactatttgatatagaaaagcagaaatattgagttcgtttacagGTTGAGAACCAAGAAGGATTAGTAAACTTCGATGACATATTGAGAGAAACAGACGGGATAATGGTAGCGCGAGGAGACCTTGGAATGGAAATTCCAATCG
upper sequence: PP1S124_70V6.2 (Physcomitrella patens), 3'ss of exon 3
lower sequence: EFJ16690 (Selaginella moellendorffii), 3'ss of exon 2
ggttttactcagtatgagacaggtttaaaattatgtgattctgcctctattcaaagaatcacaaaattgtgtcttgatcctgctttgatttctaccatagGTTGAGAATCAGGAAGGTCTGGTGAACTTCGATGACATATTGAAAGAGACAGACGGAGTCATGGTGGCAAGAGGGGACCTGGGAATGGAGATTCCTACGG
| | | || | | |||| ||| | | |||||||||| || ||||| | || ||||||||||||||||||| ||| |||||||| | ||||| || |||| ||||| |||||||| ||||| | |
-------------------------------------------------------gtactatttgatatagaaaagcagaaatattgagttcaattacagGTTGAGAACCAAGAAGGATTAGTAAACTTCGATGACATATTGAGAGAAACAGACGGGATAATGGTAGCGCGAGGAGACCTTGGAATGGAAATTCCAATTG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tctattcaaagaatcacaaaattgtgtcttgatcctgctttgatttctaccatagGTTGAGAATCAGGAAGGTCTGGTGAACTTCGATGACATATTGAAAGAGACAGACGGAGTCATGGTGGCAAGAGGGGACCTGGGAATGGAGATTCCTACGG
tttctacc CT-rich tract
acaaaatt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
ggttttactcagtatgagacaggtttaaaattatgtgattctgcctctattcaaagaatcacaaaattgtgtcttgatcctgctttgatttctaccatagGTTGAGAATCAGGAAGGTCTGGTGAACTTCGATGACATATTGAAAGAGACAGACGGAGTCATGGTGGCAAGAGGGGACCTGGGAATGGAGATTCCTACGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGTGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAT