Sequence
atgc intronic sequence ATGC exonic sequencegtgagtctcgagaatggatcttattcatcacttttcttgtgcatgacttcactgcgagctgcgttacttcgaaatgttgcaatatcaccagtatcaatatcccaattctcctcaattttgattgtgatgtcgtggttcgtgcagCTTGTGTGAGTCCAGCCGACTCAAATGCTGAGGAGACGCTGAACACACTGAAGTATGCGAATCGGGCCCGTAACATTCAGAATAAACCCACG
Basic information
species | Physcomitrella patens |
transcript | PP1S74_30V6.1 |
intron # | 7 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: PP1S74_30V6.1 (Physcomitrella patens), 3'ss of exon 7
lower sequence: GLYMA02G37800.1 (Glycine max), 3'ss of exon 7
gtgagtctcgagaatggatcttattcatcacttttcttgtgcatgacttcactgcgagctgcgttacttcgaaatgttgcaatatcaccagtatcaatatcccaattctcctcaattttgattgtgatgtcgtggttcgtgcagCTTGTGTGAGTCCAGCCGACTCAAATGCTGAGGAGACGCTGAACACACTGAAGTATGCGAATCGGGCCCGTAACATTCAGAATAAACCCACG
|| | |||| || || || || | ||| || || | | | || || | || ||| | | || |||| ||| |||||| ||||| ||||| || ||| | |||||||| ||||| ||||||| ||||||||||| || || || |||||||||||||| ||| |
--------------------------------------gtactgaactt----gctaggtggatt---ttaaaaaattacactttt--taatacacatgtatcatgtct-----aatctgtttgtaatgc---------tgcagCATGTGTTAGTCCTGCTGACACCAATGCTGAAGAGACATTGAACACTCTGAAGTATGCTAACCGTGCTCGTAACATTCAGAACAAAGCAGTT
upper sequence: PP1S74_30V6.1 (Physcomitrella patens), 3'ss of exon 7
lower sequence: GLYMA04G10080.1 (Glycine max), 3'ss of exon 6
gtgagtctcgagaatggatcttattcatcacttttcttgtgcatgacttcactgcgagctgcgttacttcgaaatgttgcaatatcaccagtatcaatatcc-caattctcctcaattttgattgtgatgtcgtggttcgtgcagCTTGTGTGAGTCCAGCCGACTCAAATGCTGAGGAGACGCTGAACACACTGAAGTATGCGAATCGGGCCCGTAACATTCAGAATAAACCCACG
| ||| || || | | ||| ||||| || | ||| | | | | | || || | | |||| | |||||| ||||| ||||| || ||| |||||||||| ||||| ||||||| | |||||||| || || || |||||||||||||| || |
------------------------------------------aaaactgtgatgataggtacaa-actc--aaatgatgagagttcagatatttttgtgttttctatagtcacatgcatcatctaacctgtcagaaatgttgcagCATGTGTTAGTCCTGCTGACACAAATGCTGAAGAGACATTGAACACTTTAAAGTATGCAAACCGTGCTCGTAACATTCAGAACAAGGCAGTT
upper sequence: PP1S74_30V6.1 (Physcomitrella patens), 3'ss of exon 7
lower sequence: GLYMA14G36030.1 (Glycine max), 3'ss of exon 7
gtgagtctcgagaatggatcttattcatcacttttcttgtgcatgacttcactgcgagctgcgttacttcgaaatgttgcaatatcaccagtatcaatatcccaattctcctcaattttgattgtgatgtcgtggttcgtgcagCTTGTGTGAGTCCAGCCGACTCAAATGCTGAGGAGACGCTGAACACACTGAAGTATGCGAATCGGGCCCGTAACATTCAGAATAAACCCACG
| | | || | || | || | | | | | | ||| || || | || || | | || ||| ||| |||||| ||||| ||||| || ||| | |||||||| ||||| ||||||| ||||||||||| || || || || ||||||||||| || |
---------------------------------------------------gtactgtacttgctaggtagatttatt-tattttttcactttttaatgtcacatgtatcatctaatctgtttggaatgc---------tgcagCATGTGTTAGTCCTGCTGACACCAATGCTGAAGAGACATTGAACACTCTGAAGTATGCTAACCGTGCTCGCAACATTCAGAACAAGGCAGTT atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.agtatcaatatcccaattctcctcaattttgattgtgatgtcgtggttcgtgcagCTTGTGTGAGTCCAGCCGACTCAAATGCTGAGGAGACGCTGAACACACTGAAGTATGCGAATCGGGCCCGTAACATTCAGAATAAACCCACG
ttttgat putative branch site (score: 4)
aattttgatt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtgagtctcgagaatggatcttattcatcacttttcttgtgcatgacttcactgcgagctgcgttacttcgaaatgttgcaatatcaccagtatcaatatcccaattctcctcaattttgattgtgatgtcgtggttcgtgcagCTTGTGTGAGTCCAGCCGACTCAAATGCTGAGGAGACGCTGAACACACTGAAGTATGCGAATCGGGCCCGTAACATTCAGAATAAACCCACG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGAAG