Sequence
atgc intronic sequence ATGC exonic sequencegtatgtttcgctactggactggtttatggattcggttcatgaaattctcaacgagttcatgacattactttctccttttgctaatgaggtgcatttgtatactcgtgtgggtcagCGTCAAGCTGCACAGTGTGTGGGACGCGTTATTCGTTCTAAAGCAGATTATGGAATGATGATTTTTGCTGACAAGAG
Basic information
species | Physcomitrella patens |
transcript | PP1S145_26V6.3 |
intron # | 11 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: PP1S145_26V6.2 (Physcomitrella patens), 3'ss of exon 11
lower sequence: LOC_Os05g05260.1 (Oryza sativa), 3'ss of exon 8
gtatgtttcgctactggactggtttatggat--tcggttcatgaaattctcaacgagttcatgacattactttctccttttgctaatgaggtgcatttgtatactcgtgtgggtcagCGTCAAGCTGCACAGTGTGTGGGACGCGTTATTCGTTCTAAAGCAGATTATGGAATGATGATTTTTGCTGACAAGAG
|| |||| | ||| | || ||| | | | | | || | | | |||| || || || | ||| | |||||||| || ||||| || || || || ||||||||||||||||||||||||||||| ||||||||||||||
----gtaataatactacttctgccaggggaaagtagggctggatgatttgtagctttatttttctagagacatccaacaaagttttcttgacat-tttggattct-gttaatgccagAGGCAAGCTGCGCAATGTGTTGGCCGTGTGATCCGTTCTAAAGCAGATTATGGAATGATGATATTTGCTGACAAGAG
upper sequence: PP1S145_26V6.2 (Physcomitrella patens), 3'ss of exon 11
lower sequence: GRMZM2G097605_T02 (Zea mays), 3'ss of exon 3
gtatgtttcgctactggactggtttatggat---tcggttca--tgaaattctcaacgagttcatgacat-----tactttctccttttgctaatgaggtgcatttgtatactcgtgtgggtcagCGTCAAGCTGCACAGTGTGTGGGACGCGTTATTCGTTCTAAAGCAGATTATGGAATGATGATTTTTGCTGACAAGAG
| ||| || | || | || || || ||| | | | ||| | || || | | || | ||||| | ||| | ||||| | ||||| || || ||||| || || |||||||| || ||||| |||||||| |||||||| ||||||||||||||
--gtaattcattattactttgaggaaaaaataactccttttgattgacacctcttatctccttatgttgtcgagatatttgtaacacaatttctcgaaataaatttgaaatctcattaatgtcagAGGCAAGCGGCCCAATGTGTCGGTCGTGTTATTCGCTCCAAAGCTGATTATGGGATGATGATATTTGCTGACAAGAG
upper sequence: PP1S145_26V6.2 (Physcomitrella patens), 3'ss of exon 11
lower sequence: GLYMA02G09080.1 (Glycine max), 3'ss of exon 9
gtatgtttcgctactggactggtttatggattcggttcatgaaattctcaacgagttcatg-acattact-ttctccttttgctaatgaggtgcatttgtatactcgtgtgggtcagCGTCAAGCTGCACAGTGTGTGGGACGCGTTATTCGTTCTAAAGCAGATTATGGAATGATGATTTTTGCTGACAAGAG
| | |||| | |||| | |||||| | |||| | || || | | | | | | | ||| | |||||||| ||||||||||| || ||||| ||||| || || ||||||||||||||||||||||| ||||| ||
--------------------------------------gtttgactctct-ctctctcatataaattactgctgataatttgatcatcagattcctaaacttttctgcttaag-cagAGACAAGCTGCTCAGTGTGTGGGTCGTGTTATCCGTTCAAAGGCTGATTATGGAATGATGATTTTTGCAGACAAAAG
upper sequence: PP1S145_26V6.2 (Physcomitrella patens), 3'ss of exon 11
lower sequence: GLYMA16G28290.1 (Glycine max), 3'ss of exon 9
gtatgtttcgctactggactggtttatggattcggttcatgaaattctcaacgagttcatgacattactttctcct-tttgctaatgaggtgcatttgtatactcgtgtgggtcagCGTCAAGCTGCACAGTGTGTGGGACGCGTTATTCGTTCTAAAGCAGATTATGGAATGATGATTTTTGCTGACAAGAG
|||| || || | | || | | |||| | || | |||||| |||| | || || | | | | | | | ||| | |||||||| || |||||||| || || || ||||| || || ||||||||||||||||||||||| ||||| ||
----gtttgactctctctctctctctctgtctctctctcta----tctctat---ctcttataattactgcagataatttgatcatcagattcctaaacttttatgcttaag-cagAGACAAGCTGCTCAATGTGTGGGTCGTGTAATCCGTTCAAAGGCTGATTATGGAATGATGATTTTTGCAGACAAAAG
upper sequence: PP1S145_26V6.2 (Physcomitrella patens), 3'ss of exon 11
lower sequence: Vv07s0104g00060.t01 (Vitis vinifera), 3'ss of exon 9
gtatgtttcgctactggactggtttatggattcggttcatgaaattct-caacgagttcatgacattactttctccttttgcta-atgaggtgcatttgtatactcgtg-tgggtcagCGTCAAGCTGCACAGTGTGTGGGACGCGTTATTCGTTCTAAAGCAGATTATGGAATGATGATTTTTGCTGACAAGAG
|||| ||| || | || | | | | || | ||| | | | | | | ||| | ||||| | |||| | || ||| ||| | ||||||||||| |||||||| || || || ||||| || ||||||||||| ||||||||||| |||||||| ||
gtattgttcactgcactctgtgtcatttagtgcaatatgcattgtttggcctttggttggttagttcatgtcttgcttaaataatatgagcttcattaatgagaatgtaatggagcagAGGCAAGCTGCACAATGTGTGGGCCGAGTAATCCGTTCAAAGGCAGATTATGGGATGATGATTTTCGCTGACAAAAG
upper sequence: PP1S145_26V6.2 (Physcomitrella patens), 3'ss of exon 11
lower sequence: EFJ08988 (Selaginella moellendorffii), 3'ss of exon 8
gtatgtttcgctactggactggtttatggattcggttcatgaaattctcaacgagttcatgacattactttctccttttgctaatgaggtgcatttgtatactcgtgtgggtcagCGTCAAGCTGCACAGTGTGTGGGACGCGTTATTCGTTCTAAAGCAGATTATGGAATGATGATTTTTGCTGACAAGAG
| ||||| | || || |||||| || ||| || ||| || ||| | |||||||| || || || || || || ||||| || ||||||||||| ||||||||||| ||||| ||||||||
--------------------------------------------------gcaagttctttacgttctgttctccgctt-------------attcgtttacctgtac----cagAGACAAGCTGCTCAATGCGTAGGCCGTGTCATTCGCTCAAAAGCAGATTACGGAATGATGATATTTGCAGACAAGAGMapped EST sequences
Showing partial alignments of ESTs and genomic sequences. See full alignments
ATGC EST sequence
ATGC genomic sequence (exon)
ATGC genomic sequence (truncated intron)
EST:
gi|37830236|gb|BJ588248.1|BJ588248EST: CTTTTCAGATTAAAGAGAATGATTTCCTGACGTTTGATGCCGTG CGTCAAGCTGCACAGTGTGTGGGACGCGTTATTCGTTCTAAAGCAGATTAT
genomic: CTTTTCAGATTAAAGAGAATGATTTCCTGACGTTTGATGCCGTGgtatgtttcg ... tgtgggtcagCGTCAAGCTGCACAGTGTGTGGGACGCGTTATTCGTTCTAAAGCAGATTAT
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.gacattactttctccttttgctaatgaggtgcatttgtatactcgtgtgggtcagCGTCAAGCTGCACAGTGTGTGGGACGCGTTATTCGTTCTAAAGCAGATTATGGAATGATGATTTTTGCTGACAAGAG
tgctaat putative branch site (score: 2)
atttgtata 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtatgtttcgctactggactggtttatggattcggttcatgaaattctcaacgagttcatgacattactttctccttttgctaatgaggtgcatttgtatactcgtgtgggtcagCGTCAAGCTGCACAGTGTGTGGGACGCGTTATTCGTTCTAAAGCAGATTATGGAATGATGATTTTTGCTGACAAGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAGAT