Sequence
atgc intronic sequence ATGC exonic sequence...aatgcattacaagcgattccaaatcttcgtcttctgagcatgattgttacgttggtgtccgaccgtttcataaagtcgtagcttattcctcatcttacagATTCTGTTCTGTCCGATGGTAGGGTCCGAAGTTTACTCATCCGAAGTTAAGAAGACGGAGGTGCTCATGGAGAATTTCCACTGC
Basic information
species | Physcomitrella patens |
transcript | PP1S40_79V6.1 |
intron # | 1 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: PP1S40_79V6.1 (Physcomitrella patens), 3'ss of exon 1
lower sequence: LOC_Os07g08170.1 (Oryza sativa), 3'ss of exon 2
--aatgcattacaagcgattccaaatcttcgtc---ttctgagcatgattgttacgttggtgtccgaccgtttcataaagtcgtagcttatt-cctcatcttacagATTCTGTTCTGTCCGATGGTAGGGTCCGAAGTTTACTCATCCGAAGTTAAGAAGACGGAGGTGCTCATGGAGAATTTCCACTGC----------------
|||| ||||| | ||| | | || || | | | | | |||| || || | | || || || |||||| | | ||||| | | |||||||| |||||||| || ||||| || || || || || ||||| || |||||||| ||||||||||||| |
tcaatgtcttacatctgcttc--atttttggtaaaacttccaatgtttcattcatgttgatgga-gaatatcttat---gtgttatcttattattttactatacagGTCCCTTTCTGTCCTATGGTAGGATCAGAAGTGTATTCCTCAGAGGTCAAGAAAACTGAGGTGCTAATGGAGAATTTCCGTAGAGCTATAGGTTTGCGTA
upper sequence: PP1S40_79V6.1 (Physcomitrella patens), 3'ss of exon 1
lower sequence: GLYMA08G21830.1 (Glycine max), 3'ss of exon 2
aatgcattacaagcgattccaaatcttcgtcttctgagcatgattgttacgttggtgtccgaccgtttcataaagtcgtagcttattcctcatcttacagATTCTGTTCTGTCCGATGGTAGGGTCCGAAGTTTACTCATCCGAAGTTAAGAAGACGGAGGTGCTCATGGAGAATTTCCACTGC----------------
| || | || || | |||| || || |||||||||| | | | | || | | || ||||||| | | ||| | | |||||| || ||||| || |||||||||||||| || ||||| |||||||| ||||| |||||||| ||||| | |
-gtttctttctcaagactctcattctttgtgtt------gtgattgttaccc------cttcttgctgcttataatta-agtttattcc--actctgcagGTACCGTTCTGCCCTATGGTTGGCTCCGAAGTTTACTCCTCGGAAGTAAAGAAGACTGAGGTTCTCATGGAAAATTTTCGACGGGCCATTGGTCTGCGTA
upper sequence: PP1S40_79V6.1 (Physcomitrella patens), 3'ss of exon 1
lower sequence: GLYMA07G02170.1 (Glycine max), 3'ss of exon 2
aatgcattacaagcgattccaaatctt----cgtcttctgagcatgattgttacgttggtgtccgaccgtttcataaagtcgtagcttattcctcatcttacagATTCTGTTCTGTCCGATGGTAGGGTCCGAAGTTTACTCATCCGAAGTTAAGAAGACGGAGGTGCTCATGGAGAATTTCCACTGC----------------
| | || || | ||| || || | | |||| | | ||| || | | | | || | | || | ||| ||| ||||| || ||||| || || ||||||||||| || ||||| |||||||| ||||| |||||||| ||||| |
-gtttccctctcaagactctcattctcgtggtgttttttttttctctgtgttttgattgtgacccttcttgctgctga-taataatgtttatgccactctgcagGTTCCTTTCTGCCCAATGGTTGGTTCTGAAGTTTACTCCTCAGAAGTAAAGAAGACCGAGGTTCTCATGGAAAATTTTAGACGGGCCATTGGTCTGCGTA
upper sequence: PP1S40_79V6.1 (Physcomitrella patens), 3'ss of exon 1
lower sequence: AT5G22330.1 (Arabidopsis thaliana), 3'ss of exon 2
--aatgcattacaagcgattccaaatcttcgtcttctgagcat-----gattgttacgttggtgtccgaccgtttcataaagtcgtagcttattcc-------------tcatcttacagATTCTGTTCTGTCCGATGGTAGGGTCCGAAGTTTACTCATCCGAAGTTAAGAAGACGGAGGTGCTCATGGAGAATTTCCACTGC----------------
||| | ||| |||||| | | | | || | | | ||| | |||| | | | ||||||||| |||| ||| ||| |||||||| ||||| || || || ||||||||||| || |||||||| || ||||| |||||||||||||| |
gtaattttggatgtctcattttgtatcttctttgttacattgtttccacatggcttcattgtatgaagcttttttcttttacttttagcttattttatctggattgtttctttcttgcagGTTCCATTCTGTCCAATGGTTGGATCTGAGGTTTACTCATCAGAGGTTAAGAAAACAGAGGTTCTCATGGAGAATTTTAGACGTGCCATTGGTCTACGTA atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.gttacgttggtgtccgaccgtttcataaagtcgtagcttattcctcatcttacagATTCTGTTCTGTCCGATGGTAGGGTCCGAAGTTTACTCATCCGAAGTTAAGAAGACGGAGGTGCTCATGGAGAATTTCCACTGC
cttattcctcatctt CT-rich tract
tttcataaa 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
aatgcattacaagcgattccaaatcttcgtcttctgagcatgattgttacgttggtgtccgaccgtttcataaagtcgtagcttattcctcatcttacagATTCTGTTCTGTCCGATGGTAGGGTCCGAAGTTTACTCATCCGAAGTTAAGAAGACGGAGGTGCTCATGGAGAATTTCCACTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAA