Sequence
atgc intronic sequence ATGC exonic sequence...acacctagttgtcctgctgttttagggtattcaaaaacttcattgttattcaataatgattctgtattctgcgcagctaacatgaatgtaacgtgtgcagTATTTGGTCCAATCAGCGATTGATGGGTACAATGTCTGTATTTTTGCATACGGACAAACTGGATCAGGGAAAACTTTTACTATTTATGGTTCTGAAAATA
Basic information
species | Physcomitrella patens |
transcript | PP1S83_25V6.1 |
intron # | 19 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: PP1S83_25V6.1 (Physcomitrella patens), 3'ss of exon 19
lower sequence: LOC_Os04g57140.2 (Oryza sativa), 3'ss of exon 18
--acacctagttgtcctgctgttttagggtattcaaaaacttcattgttattcaataatgattctgtattctgcgcagctaacatgaatgtaacgtgtgcagTATTTGGTCCAATCAGCGATTGATGGGTACAATGTCTGTATTTTTGCATACGGACAAACTGGATCAGGGAAAACTTTTACTATTTATGGTTCTGAAAATA
| | || | || ||| || || || | | | | ||| || | || | || ||||||| | | |||||||| | || ||||| || ||||||| || ||||| ||||| ||||| || || |||||||| || || ||||||||||| |||||||| |||||||| |
gtgaccttttttttaacacttctttttaacatacatgtgctcattagattatttgcaat-----tggactccatgtgtttatcatgaattttgtg-atgcagTATCTAGTTCAATCGGCCGTTGATGGATATAATGTTTGTATATTTGCTTATGGGCAAACTGGTTCTGGAAAAACTTTTACAATTTATGGATCTGAAAACA
upper sequence: PP1S83_25V6.1 (Physcomitrella patens), 3'ss of exon 19
lower sequence: GRMZM2G070273_T01 (Zea mays), 3'ss of exon 17
-------------------------------------------acacctagttgtcctgctgttttagggtattcaaaaacttcattgttattcaataatgattctgtattctgcgcagctaacatgaatgtaacgtgtgcagTATTTGGTCCAATCAGCGATTGATGGGTACAATGTCTGTATTTTTGCATACGGACAAACTGGATCAGGGAAAACTTTTACTATTTATGGTTCTGAAAATA
| || | || | || | |||| | | ||| | | || | ||| || || ||||| || |||||||| |||| |||||||| ||||||| || ||||||||||| ||||| || || |||||||| || || || ||||| |||||||||||||| ||||| |
gtgaatatttcaaatgctatcttttgtgttgatgccgtcggtaatacaaattttatttctaagattgttggcttcatatgatctgttg--aatttatgttcattttgggtttcatatgatctgt-tgaatttatgtgatgcagTATCTGGTACAATCAGCTGTTGATGGATATAATGTCTGTATATTTGCGTATGGCCAAACTGGTTCTGGAAAGACTTTCACTATTTATGGTTCAGAAAACA
upper sequence: PP1S83_25V6.1 (Physcomitrella patens), 3'ss of exon 19
lower sequence: GRMZM2G423861_T02 (Zea mays), 3'ss of exon 17
------acacctagttgt-cctgctgttttagggtattcaaaaacttcattgttattc--aataatgatt-ctgtattctgcgca-gctaacatgaatgtaacgtgtgcagTATTTGGTCCAATCAGCGATTGATGGGTACAATGTCTGTATTTTTGCATACGGACAAACTGGATCAGGGAAAACTTTTACTATTTATGGTTCTGAAAATA
| | | | | || ||| || | ||| || | | | ||||| | | || | ||| | | | | | ||||| || ||||||| |||| |||||||| ||||||| || || || || || |||||||| || |||||||| || || || ||||| |||||||||||||| || || |
gtgaatatttcaaatgctatcttttgtgttgatgccatcagtaatataaattttatttctaggactgttcactgagggtttcatatgatgtgttgaatttatgtgatgcagTACCTGGTACAATCAGCTGTTGATGGATATAACGTTTGCATATTTGCATATGGTCAAACTGGTTCTGGAAAGACTTTCACTATTTATGGTTCAGATAACA atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ttattcaataatgattctgtattctgcgcagctaacatgaatgtaacgtgtgcagTATTTGGTCCAATCAGCGATTGATGGGTACAATGTCTGTATTTTTGCATACGGACAAACTGGATCAGGGAAAACTTTTACTATTTATGGTTCTGAAAATA
aataatgatt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
acacctagttgtcctgctgttttagggtattcaaaaacttcattgttattcaataatgattctgtattctgcgcagctaacatgaatgtaacgtgtgcagTATTTGGTCCAATCAGCGATTGATGGGTACAATGTCTGTATTTTTGCATACGGACAAACTGGATCAGGGAAAACTTTTACTATTTATGGTTCTGAAAATA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ctgcgca