Sequence
atgc intronic sequence ATGC exonic sequence...tatcagtttgccctcacgaaaagtaattatgataccacgacgtgagcttaagtttctgatcatgtgcccttaggctaaatattgtaagcgcttcgtgcagTTACTTCTCATATGAACATTTTTATGTCATATATTGCAAGTTCTGGGAGCTGGATTCAGATCACGATTTTTTAATAGACAAAGATGATCTCCTTCGATAT
Basic information
species | Physcomitrella patens |
transcript | PP1S7_163V6.1 |
intron # | 7 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: PP1S7_163V6.1 (Physcomitrella patens), 3'ss of exon 7
lower sequence: LOC_Os02g09840.1 (Oryza sativa), 3'ss of exon 6
------tatcag----tttgccctcacgaaaa----gtaattatgataccacgacgtgagcttaagtttctgatcatgtgcccttaggctaaatattgta--agcgcttc--------gtgcagTTACTTCTCATATGAACATTTTTATGTCATATATTGCAAGTTCTGGGAGCTGGATTCAGATCACGATTTTTTAATAGACAAAGATGATCTCCTTCGATAT
|| | |||| |||| | || | | | | | | | ||| | || | | || || | | | | | ||| || || || ||||||||||| ||||||||||| |||||||||||||||||||||||||| |||| || ||||| || || || ||||| |||| || |||
gtgagacattaaagcatttggtttcacattatctttgttgcttctctcctctcttatagttgttattctctttttttggggctctacaacaagtgcggcactaaagtttctcatttttgtatagGTATTTCTCATATGAGCATTTTTATGTGATATATTGCAAGTTCTGGGAGCTGGACACAGACCATGATTTCTTCATTGATAAAGAAAATCTTATTAAGTAT
upper sequence: PP1S7_163V6.1 (Physcomitrella patens), 3'ss of exon 7
lower sequence: LOC_Os10g33680.1 (Oryza sativa), 3'ss of exon 7
tatcagtttgccctcacgaaaagta-attatgataccacgacgtgagcttaagtttctg-atcatgtgcccttaggc-taaatattgtaagcgcttcgtgcagTTACTTCTCATATGAACATTTTTATGTCATATATTGCAAGTTCTGGGAGCTGGATTCAGATCACGATTTTTTAATAGACAAAGATGATCTCCTTCGATAT
| || | | || || ||||| ||| | | | ||| | || | | || | | | ||| || | | || | ||||| ||||||||||| || || |||||||| ||||| ||||| || |||||| |||| ||||||| |||||||| || || ||||| | || | |||||
--acgaattacttggattcaagttatattatttatgtgcgaatcaaacaagattttttacattttttttccaaatgtgttaattttctga-tgcctaatgcagATACTTCTCATACGAGCACTTTTATGTGATATACTGCAAATTTTGGGAGTTGGACACAGATCATGATTTTTTGATTGATAAAGAGAACCTTATCAGATAT
upper sequence: PP1S7_163V6.1 (Physcomitrella patens), 3'ss of exon 7
lower sequence: GRMZM2G104254_T02 (Zea mays), 3'ss of exon 3
tatcagtttgccctcacgaaaagtaattatgataccacgacgtgagcttaagtttctgatcatgtgcccttag--gctaaatattgtaagcgcttcg-tgcagTTACTTCTCATATGAACATTTTTATGTCATATATTGCAAGTTCTGGGAGCTGGATTCAGATCACGATTTTTTAATAGACAAAGATGATCTCCTTCGATAT
| | || | | | | || || | | | | || || || |||| | | | ||| | | | | | | ||||| |||||||||||||| || |||||||| || |||||||| ||||||||||||||| |||| ||||||||||| || || || || | ||| | ||||
---cggattacatttgttcacgctgttttctttatatagtcttaacagtattctttgtataatgtttgccaaattgataatcttggctcgtgatctgatgcagATACTTCTCATATGAGCACTTTTATGTGATCTATTGCAAATTCTGGGAGCTGGATGCAGACCACGATTTTTTGATTGATAAGGAGAACCTCATCAAATAT
upper sequence: PP1S7_163V6.1 (Physcomitrella patens), 3'ss of exon 7
lower sequence: GRMZM2G148323_T01 (Zea mays), 3'ss of exon 7
-tatcagttt-gccctcacgaaaagtaatta-tgataccacgacgtgagcttaagtttctgatcatgtgcccttaggctaaatattgtaagcgcttcgtgcagTTACTTCTCATATGAACATTTTTATGTCATATATTGCAAGTTCTGGGAGCTGGATTCAGATCACGATTTTTTAATAGACAAAGATGATCTCCTTCGATAT
|| |||| | | | | | | | || | | | | ||||| | | | || | || || || | |||| | | | | | |||||| || |||||||||||||| |||||||| || || ||||| ||||||||||||||| |||| ||||||||||| || || || || ||||| | ||||
ccatttgttttgtgtggattacatttgttcactgttttctttatatagtcttaactgtgt-ataacgtttactgag--ttaataatcttggatcatggtgcagATATTTCTCATATGAACACTTTTATGTGATCTACTGCAAATTCTGGGAGCTGGATGCAGACCACGATTTTTTGATTGATAAGGAAAATCTCATCAAATAT
upper sequence: PP1S7_163V6.1 (Physcomitrella patens), 3'ss of exon 7
lower sequence: GRMZM2G040094_T01 (Zea mays), 3'ss of exon 6
-------------------------------tatcagtttgccctcacgaaaagt---aattatgataccacg--acgtgagcttaagtttctgatcatgtgcc--cttaggctaaatattgtaagcgcttcg-tgcagTTACTTCTCATATGAACATTTTTATGTCATATATTGCAAGTTCTGGGAGCTGGATTCAGATCACGATTTTTTAATAGACAAAGATGATCTCCTTCGATAT
| |||| | || ||| | || | | | | | || | | | | || ||| | || || |||||| | | | || || |||||||||||||| ||||| ||||| |||||||||||||||||||| ||||| |||| ||||| || || || |||||||| |||| || |||
gtgacaccttcaaatcaagtcctaacaattcccttcctttgtatttacaaaatttctcaagtgcagtttttctttaggggaaccctaaactttcattatgcaacacattgaact---tattgtttgttttcccctgtagATACTTCTCATATGAGCATTTCTATGTGATATATTGCAAGTTCTGGGAACTGGACACAGACCACGACTTCTTTATTGACAAAGAAAATCTTATTAAGTAT
upper sequence: PP1S7_163V6.1 (Physcomitrella patens), 3'ss of exon 7
lower sequence: GRMZM2G080083_T02 (Zea mays), 3'ss of exon 6
----------------------tatcagtt-tgccctcacgaaaagt---aattatgata---ccacgacgtgagcttaagtttctgatcatgtgcccttaggctaaa--tattgtaagcgcttcg-tgcagTTACTTCTCATATGAACATTTTTATGTCATATATTGCAAGTTCTGGGAGCTGGATTCAGATCACGATTTTTTAATAGACAAAGATGATCTCCTTCGATAT
|| ||||| ||| | | | | || | | | | | | | | |||| ||| || ||| | | || || | |||| | | ||| || || || ||||||||||| ||||| ||||| |||||||||||||||||||||||||| | ||||| || || || || |||||||| |||| || |||
gtgacaccttcaaatcatgttctaacagttctgctcctttgtattttctcaagtgcagtttttcttcaatggaaccctaagcttcc-attatgcaac---acactgaacttcttgtttgtgtttccctgtagGTATTTCTCATATGAGCATTTCTATGTGATATATTGCAAGTTCTGGGAGCTGGACACCGATCATGACTTCTTTATTGACAAAGAAAATCTTATTAAGTAT
upper sequence: PP1S7_163V6.1 (Physcomitrella patens), 3'ss of exon 7
lower sequence: GLYMA10G30930.1 (Glycine max), 3'ss of exon 7
-----tatcagtttgccctcacgaaaagta-attatgataccacgacgtgagcttaagtttctgatcat---gtgcccttaggctaaatattgta----agcgcttcgtgcagTTACTTCTCATATGAACATTTTTATGTCATATATTGCAAGTTCTGGGAGCTGGATTCAGATCACGATTTTTTAATAGACAAAGATGATCTCCTTCGATAT
||| | ||| ||| | | |||| | | || | |||| ||| | || | || | || | | || || |||||||| ||||| ||||||||||| ||||| ||||| || |||||||||||| ||||||||||||| |||||||||||||| |||| | |||||
gtagatatactatcattatcattaaattcacacaatgactctgtttttcagccaaaatatattgataccagaatgcattgagtgtttttactttacctaataattgtctgtagGTACTTCTCTTATGAGCATTTTTATGTTATATACTGCAAATTTTGGGAGCTGGATACAGATCACGATTTCTTAATAGACAAAGAGAATCTTATCAGATAT
upper sequence: PP1S7_163V6.1 (Physcomitrella patens), 3'ss of exon 7
lower sequence: GLYMA19G43790.1 (Glycine max), 3'ss of exon 7
-----------------tatcagtttgccc--tcacgaaaagtaattatgataccacgac----gtgagcttaa-gtttctg-atcatgtgcccttaggct-----aaatattgtaagcgcttcgtgcagTTACTTCTCATATGAACATTTTTATGTCATATATTGCAAGTTCTGGGAGCTGGATTCAGATCACGATTTTTTAATAGACAAAGATGATCTCCTTCGATAT
| ||| || | ||| | | || | || | ||| || || | | || || ||| ||||| || | | | | | | | ||||| |||||||| ||||| ||||||||||| ||||| |||||||| |||||||||||| ||||||| ||||| || ||||||||||| ||||| | |||||
gtagatataattgaaaatgtcatttcaattaacttcagaaaatgaccttggtgtcattattcaaatgaactaaatatatttgtattatgatgccttaatcttttttacctttccttaatgttatctgcagGTACTTCTCTTATGAGCATTTTTATGTTATATACTGCAAGTTTTGGGAGCTGGATACAGATCATGATTTCTTGATAGACAAAGAGAATCTCATCAGATAT
upper sequence: PP1S7_163V6.1 (Physcomitrella patens), 3'ss of exon 7
lower sequence: GLYMA20G36530.1 (Glycine max), 3'ss of exon 7
-------tatcagtttgccctcacgaaaa-gtaattatgataccacgacgtgagcttaagtttctgatcatgtgcccttaggctaaatattg--taagcgcttcgtgcagTTACTTCTCATATGAACATTTTTATGTCATATATTGCAAGTTCTGGGAGCTGGATTCAGATCACGATTTTTTAATAGACAAAGATGATCTCCTTCGATAT
|| | || | | | | ||| | | | | || || | | | ||| | | | | | ||| | || || |||||||| ||||| ||||||||||| ||||| ||||| || |||||||||||| ||||||||||||| || ||||||||||| |||| | |||||
gtagatatactatattatcattaaattcacacaatgactctgtttttcagccaaaatatattcataacaaaatgcattgtgtttttacttcacctaataattgtctgtagGTACTTCTCTTATGAGCATTTTTATGTTATATACTGCAAATTTTGGGAGCTGGATACAGATCACGATTTCTTTATAGACAAAGAGAATCTTATCAGATAT
upper sequence: PP1S7_163V6.1 (Physcomitrella patens), 3'ss of exon 7
lower sequence: GLYMA03G41180.1 (Glycine max), 3'ss of exon 7
-----------------tatcagtttgccc--tcacgaaaagtaattatgataccacgacgtgagc---ttaagt---ttctgatcatgtgcccttaggct-----aaatattgtaagcgcttcgtgcagTTACTTCTCATATGAACATTTTTATGTCATATATTGCAAGTTCTGGGAGCTGGATTCAGATCACGATTTTTTAATAGACAAAGATGATCTCCTTCGATAT
| ||| || | ||| | | || | || | | | ||| | || || ||| ||||| || | | | ||| | ||||| |||||||| || || ||||||||||| ||||| |||||||| |||||||||||| ||||||| ||||| || ||||||||||| ||||| | |||||
gtagatataattgaaaatttcatttcaattaacttcagaaaatgaccttggtttcattattcaaacgaactaaatatatttgtattatgatgccttaatcttttttacctttcctaaatattatctgcagGTACTTCTCTTACGAGCATTTTTATGTTATATACTGCAAGTTTTGGGAGCTGGATACAGATCATGATTTCTTGATAGACAAAGAGAATCTCATCAGATAT
upper sequence: PP1S7_163V6.1 (Physcomitrella patens), 3'ss of exon 7
lower sequence: GLYMA20G35090.1 (Glycine max), 3'ss of exon 7
----tatcagtttgccctcacga--aaagtaattatgataccacgacgtgagcttaagtttctgatcatgtgcccttaggctaaatattgtaagcgcttcgtgcagTTACTTCTCATATGAACATTTTTATGTCATATATTGCAAGTTCTGGGAGCTGGATTCAGATCACGATTTTTTAATAGACAAAGATGATCTCCTTCGATAT
| || | ||| || || || | | | | || | ||| | || ||| ||| ||| || | || ||| |||||||||||||| |||||||||||||| || ||||| || |||||||| || ||||||| || ||||| || || | ||| | || || ||||
aaattcatgattgactttcattttcaatttagttctctctgtagaattgaaattttcttgtctttttatttgcttc---attaattatcttacggaattt---cagGTACTTCTCATATGAGCATTTTTATGTCATTTACTGCAAATTTTGGGAGCTCGACACAGATCATGACTTTTTCATTGATAGAGAGAACCTTATTAAATAT
upper sequence: PP1S7_163V6.1 (Physcomitrella patens), 3'ss of exon 7
lower sequence: GLYMA10G32500.1 (Glycine max), 3'ss of exon 7
-tatcagtttgccctcacgaaaagtaattatgataccacgacgtgagcttaagtttctgatcat-gtgccc-ttaggctaaatattgtaagcgcttcgtgcagTTACTTCTCATATGAACATTTTTATGTCATATATTGCAAGTTCTGGGAGCTGGATTCAGATCACGATTTTTTAATAGACAAAGATGATCTCCTTCGATAT
||| | | |||| | | | | | || ||||| || | || | ||| ||| || | || ||| |||||||||||||| |||||||||||||| || ||||| || |||||||| || ||||||| || ||||| || || | ||| | || || ||||
aaatccatgattgactttcattttcaatttagttctctctgtagaattgaaattttcttgtctttgtatttgcttcattaattatcttacgaaattt---cagGTACTTCTCATATGAGCATTTTTATGTCATTTACTGCAAATTTTGGGAGCTCGACACAGATCATGACTTTTTCATTGATAGAGAGAACCTTATTAAATAT
upper sequence: PP1S7_163V6.1 (Physcomitrella patens), 3'ss of exon 7
lower sequence: AT1G54450.1 (Arabidopsis thaliana), 3'ss of exon 7
tatcagtttgccctcacgaaaagtaattatgataccacgacgtgagcttaagtttctgatcatgtgcccttaggctaaatattgtaagcgcttcgtgcagTTACTTCTCATATGAACATTTTTATGTCATATATTGCAAGTTCTGGGAGCTGGATTCAGATCACGATTTTTTAATAGACAAAGATGATCTCCTTCGATAT
||| || || | |||||| | ||| || | || || | || ||| | || | | | | || | || |||||||| ||||||||||| ||||||||||| ||||||||||||||| ||||| ||||||| ||||| ||||| |||||||| ||||| | ||||||
------gttggtgtctt-aagattaatta-------gtaatatgaaattgg--tgcttattaacggctttta---ttaagactctctactgtttat-tagGTACTTCTCGTATGAACATTTCTATGTCATATACTGCAAGTTCTGGGAGTTGGATACAGATCATGATTTCTTAATCGACAAAGAGAATCTCATCCGATAT
upper sequence: PP1S7_163V6.1 (Physcomitrella patens), 3'ss of exon 7
lower sequence: AT5G28850.1 (Arabidopsis thaliana), 3'ss of exon 6
tatcagtttgccctcacgaaaagtaattatgataccacgacgtgagcttaagtttctgatcatgtgcccttaggctaaatattgtaagcgcttcg---tgcagTTACTTCTCATATGAACATTTTTATGTCATATATTGCAAGTTCTGGGAGCTGGATTCAGATCACGATTTTTTAATAGACAAAGATGATCTCCTTCGATAT
| || || |||| |||| | | | || || | | || | || | ||| | | | || || ||| | || |||||||||||||| ||||| ||||||||||| ||||||||||||||||||||| | ||||||||||| | || |||||||| |||| | |||||
---------gtactgacaaaaacaaattt--gtgctattgt-tgtatatatggtattgtttctgctcatttaacatgacttttctacttactttggcaaatagATACTTCTCATATGAGCATTTCTATGTCATATACTGCAAGTTCTGGGAGCTGGATACGGATCACGATTTCCTGATTGACAAAGAAAATCTTATGAGATAT
upper sequence: PP1S7_163V6.1 (Physcomitrella patens), 3'ss of exon 7
lower sequence: AT5G28900.1 (Arabidopsis thaliana), 3'ss of exon 7
tatcagtttgccctcacgaaaagtaattatgataccacgacgtgagcttaagtttctgatcatgtgcccttaggctaaatattgtaagcgcttcg---tgcagTTACTTCTCATATGAACATTTTTATGTCATATATTGCAAGTTCTGGGAGCTGGATTCAGATCACGATTTTTTAATAGACAAAGATGATCTCCTTCGATAT
| || || |||| || || | | | | || ||| | || | || | ||| | | | || || | ||| | || |||||||| ||||| ||||| ||||||||||| ||||||||||||||||||||| | ||||||||||| | || |||||||| |||| | ||||||
---------gtactgacaaaaa-tatttgcg-tgctattgt-tgtatttatagtattgtttttgctcatttaacatcacttttctattcactttggcaattagATACTTCTCGTATGAGCATTTCTATGTCATATACTGCAAGTTCTGGGAGCTGGATACGGATCACGATTTCCTGATTGACAAAGAAAATCTTATGCGATAT
upper sequence: PP1S7_163V6.1 (Physcomitrella patens), 3'ss of exon 7
lower sequence: Vv07s0005g03730.t01 (Vitis vinifera), 3'ss of exon 8
--tatcagtttgccctcacgaaaagtaattatgataccacgacgtgagcttaa-gtttctgatcatgtgcccttaggctaaatattgtaagcgcttcgtgcagTTACTTCTCATATGAACATTTTTATGTCATATATTGCAAGTTCTGGGAGCTGGATTCAGATCACGATTTTTTAATAGACAAAGATGATCTCCTTCGATAT
| ||| | | || | | | || || | || | | | | || ||| |||| ||| ||||| || | | | | | ||||| ||||| || |||||||| || ||||| ||||| |||||||||||||||||||| ||||||| ||||| || || |||||||| ||||| | |||||
aacaacagagagaca-catgcata-tatttgttttattattagattaactagttatttatgatgatgaattgctaggccccatgtcttcacttcaac-tgcagGTACTTTTCTTATGAACACTTCTATGTTATATACTGCAAGTTCTGGGAGCTGGACACAGATCATGATTTCTTGATTGACAAAGAGAATCTCATCAGATAT
upper sequence: PP1S7_163V6.1 (Physcomitrella patens), 3'ss of exon 7
lower sequence: Vv14s0036g00750.t01 (Vitis vinifera), 3'ss of exon 4
tatcagtttgccctcacgaaaagtaattatgatac-cacgacgtgagcttaagtttctgatcatgtgcccttaggctaaatattgtaagcgcttcgtgcagTTACTTCTCATATGAACATTTTTATGTCATATATTGCAAGTTCTGGGAGCTGGATTCAGATCACGATTTTTTAATAGACAAAGATGATCTCCTTCGATAT
||| || | | | | | | || | | || ||| |||| || | | | | || | | | || || ||| || |||||||| |||||||| || ||||| ||||| ||||||||||||||||||||| | || || |||||||| || || ||||| | || | |||||
tatttgtgggaatactctcataacatttttagcatgtactgtgtggtattaaaattttaacaccattgcttttttttttttgat-tatgcccttaccatagGTACTTCTCTTATGAACACTTCTATGTTATATACTGCAAGTTCTGGGAGCTGGATACCGACCATGATTTTTTGATTGATAAAGAGAACCTAATCAGATATMapped 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|162155853|gb|FC332402.1|FC332402EST: GCTGCTCTTCAGCAAGTGGATGAAGAGGAAGACATCAACAAAGTGTTACG TTACTTCTCATATGAACATTTTTATGTCATATATTGCAAGTTCTGGGAGCT
genomic: GCTGCTCTTCAGCAAGTGGATGAAGAGGAAGACATCAACAAAGTGTTACGgtaagcattg ... cttcgtgcagTTACTTCTCATATGAACATTTTTATGTCATATATTGCAAGTTCTGGGAGCT
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.gcttaagtttctgatcatgtgcccttaggctaaatattgtaagcgcttcgtgcagTTACTTCTCATATGAACATTTTTATGTCATATATTGCAAGTTCTGGGAGCTGGATTCAGATCACGATTTTTTAATAGACAAAGATGATCTCCTTCGATAT
ggctaaa putative branch site (score: 3)
taaatattgtaa 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
tatcagtttgccctcacgaaaagtaattatgataccacgacgtgagcttaagtttctgatcatgtgcccttaggctaaatattgtaagcgcttcgtgcagTTACTTCTCATATGAACATTTTTATGTCATATATTGCAAGTTCTGGGAGCTGGATTCAGATCACGATTTTTTAATAGACAAAGATGATCTCCTTCGATAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGATCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGATG