Sequence
atgc intronic sequence ATGC exonic sequence...tttaaagtttgatatttgcttctagtttagcttttagaatttgtgacccttacacacgagtccggtgatgtgatcgttcctgaaacttttgcttcttcagACCTTGTAGCGATTGAGGAGCGTATGCGTACTGTGAAACACAAAATTCTAGTTTTGTCTGGAAAAGGAGGAGTTGGCAAGAGCACATTTGCTGCACAGCT
Basic information
species | Physcomitrella patens |
transcript | PP1S61_191V6.2 |
intron # | 2 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: PP1S61_191V6.1 (Physcomitrella patens), 3'ss of exon 3
lower sequence: GRMZM2G097190_T01 (Zea mays), 3'ss of exon 2
tttaaagtttgatatttgcttctagtttagcttttagaatttg--tgacccttacacacgagtccgg-tgatgtgatc--gttcctgaaacttttgcttcttcagACCTTGTAGCGATTGAGGAGCGTATGCGTACTGTGAAACACAAAATTCTAGTTTTGTCTGGAAAAGGAGGAGTTGGCAAGAGCACATTTGCTGCACAGCT
|| | | | |||| | | |||| || | | | | | || | | || | | || ||| || || | |||| | || || |||| ||| | || |||||||||||||||| | |||||||||||||||| ||||| ||||| ||||||||||| | || || ||
-----ggtgagtgaatgaactctatatacatgggcactatttacatggtgcctgtatatctgctaggctaaagtaaactgattattgactggttgtattttgcagATGTGGTTGCTATTGTTGAGAGGTTGGCTACTGTGAAACACAAATTATTAGTTTTGTCTGGAAAGGGAGGTGTTGGAAAGAGCACATTCTCAGCCCAACT
upper sequence: PP1S61_191V6.1 (Physcomitrella patens), 3'ss of exon 3
lower sequence: GRMZM2G031496_T01 (Zea mays), 3'ss of exon 2
-tttaaagtttgatatttgcttctagtttagctt--ttagaatttgtgacccttacacacgagtccggtgatgtgatcgttcctgaaacttttgcttcttcagACCTTGTAGCGATTGAGGAGCGTATGCGTACTGTGAAACACAAAATTCTAGTTTTGTCTGGAAAAGGAGGAGTTGGCAAGAGCACATTTGCTGCACAGCT
| || | | ||| | | | | || || |||| | | | |||| |||| ||| || || || | |||| | || || |||| ||| | || |||||||||||||||| | |||||||||||||||| ||||| ||||| || |||||||| | || || ||
agtgaatgaattgtatatacgtgggacactgtttacttgctgcttgtatagtgtctgctaggtgaaagtgaactgattgtt---gactggttgtattttgcagATGTGGTTGCTATTGTTGAGAGGTTGGCTACTGTGAAACACAAATTGTTAGTTTTGTCTGGAAAGGGAGGTGTTGGAAAAAGCACATTCTCAGCCCAACT
upper sequence: PP1S61_191V6.1 (Physcomitrella patens), 3'ss of exon 3
lower sequence: GLYMA17G34650.1 (Glycine max), 3'ss of exon 3
---tttaaagtttgatatttgcttctagtttagcttttagaatttg--tgacccttacacacgagtccggtgatgtgatcgttcctgaaacttttgcttcttcagACCTTGTAGCGATTGAGGAGCGTATGCGTACTGTGAAACACAAAATTCTAGTTTTGTCTGGAAAAGGAGGAGTTGGCAAGAGCACATTTGCTGCACAGCT
| || |||||| || || | | |||| ||| | || | | | | | || || || || | | |||| |||| |||| || || || |||| || | ||| |||||||||||| || || | || ||||| ||||| |||||||||||||||||||| || |||| || ||
ttagtcttagattgatagggcattttaa---aatgtcgagaaattgaattgccttcatatataaaatttttggtgacattgtctcctgca--tttgtttctgcagATCTGGTTGCCATTGCAGAAAGAATGGCTACTGTGAAACATAAGATATTGGTCTTGTCAGGAAAGGGAGGAGTTGGCAAGAGCACGTTCTCTGCCCAACT
upper sequence: PP1S61_191V6.1 (Physcomitrella patens), 3'ss of exon 3
lower sequence: AT5G50960.1 (Arabidopsis thaliana), 3'ss of exon 2
-tttaaagtttgatatttgcttctagtttagcttttagaatttgtgacccttacacacgagtccggtgatgtgatcgttcctgaaacttt-tgcttctt-cagACCTTGTAGCGATTGAGGAGCGTATGCGTACTGTGAAACACAAAATTCTAGTTTTGTCTGGAAAAGGAGGAGTTGGCAAGAGCACATTTGCTGCACAGCT
||| || | || | || || || || | |||| | | | || ||| | | | | | |||| | | || || | ||| | || || || | ||| | ||| | ||||| || ||||| ||||| ||||||||||| ||||| |||||||| ||||| || || | || |||||
tttttaatgctaatgtctgatttaagc---gccagatgtgtttgagtcgcagactcacttggttactagttgaagttatgctgacgttctctgttttatgtagATTTGGTTGCCATAGCAGAGAGGATGAGCACTGTTAAGCACAAGATTCTGGTTTTGTCTGGCAAAGGTGGAGTTGGTAAGAGTACTTTCTCAGCTCAGCTMapped 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|208356420|gb|DC914296.1|DC914296EST: GTGTCCTAACCAGCAAATATGTGCTACTGCTCCTAAAGGACCAGATCCAG ACCTTGTAGCGATTGAGGAGCGTATGCGTACTGTGAAACACAAAATTCTAG
genomic: GTGTCCTAACCAGCAAATATGTGCTACTGCTCCTAAAGGACCAGATCCAGgtgtgccatt ... gcttcttcagACCTTGTAGCGATTGAGGAGCGTATGCGTACTGTGAAACACAAAATTCTAG
EST:
gi|100389931|gb|BY971283.1|BY971283EST: GTGTCCTAACCAGCAAATATGTGCTACTGCTCCTAAAGGACCAGATCCAG ACCTTGTAGCGATTGAGGAGCGTATGCGTACTGTGAAACACAAAATTCTAG
genomic: GTGTCCTAACCAGCAAATATGTGCTACTGCTCCTAAAGGACCAGATCCAGgtgtgccatt ... gcttcttcagACCTTGTAGCGATTGAGGAGCGTATGCGTACTGTGAAACACAAAATTCTAG
EST:
gi|208389876|gb|DC937707.1|DC937707EST: GTGTCCTAACCAGCAAATATGTGCTACTGCTCCTAAAGGACCAGATCCAG ACCTTGTAGCGATTGAGGAGCGTATGCGTACTGTGAAACACAAAATTCTAG
genomic: GTGTCCTAACCAGCAAATATGTGCTACTGCTCCTAAAGGACCAGATCCAGgtgtgccatt ... gcttcttcagACCTTGTAGCGATTGAGGAGCGTATGCGTACTGTGAAACACAAAATTCTAG
EST:
gi|100436255|gb|BY961125.1|BY961125EST: GTGTCCTAACCAGCAAATATGTGCTACTGCTCCTAAAGGACCAGATCCAG ACCTTGTAACGATTGAGGAGCGTATGCGTACTGTGAAACACAAAATTCTAG
genomic: GTGTCCTAACCAGCAAATATGTGCTACTGCTCCTAAAGGACCAGATCCAGgtgtgccatt ... gcttcttcagACCTTGTAGCGATTGAGGAGCGTATGCGTACTGTGAAACACAAAATTCTAG
EST:
gi|100411911|gb|BY992401.1|BY992401EST: GTGTCCTAACCAGCAAATATGTGCTACTGCTCCTAAAGGACCAGATCCAG ACCTTGTAGCGATTGAGGAGCGTATGCGTACTGTGAAACACAAAATTCTAG
genomic: GTGTCCTAACCAGCAAATATGTGCTACTGCTCCTAAAGGACCAGATCCAGgtgtgccatt ... gcttcttcagACCTTGTAGCGATTGAGGAGCGTATGCGTACTGTGAAACACAAAATTCTAG
RNA-Seq data
ATGC Supported by RNA-Seq exonic block that spans over the splice site
atgs Truncated intron sequence
Each block is as long as the maximal overhang of any read spanning the junction.
The score is the number of alignments spanning the junction.
Found data for 1 RNA-Seqlibrary.
Block sizes:
30 (upstream exon),
25 (downstream exon)
Score:
6TGTCCTGGGACGGAGGCTGAACAGGCCGGGAAAGCGTCAGCATGCGAGGGGTGTCCTAACCAGCAAATATGTGCTACTGCTCCTAAAGGACCAGATCCAGgtgtgccatt ... gcttcttcagACCTTGTAGCGATTGAGGAGCGTATGCGTACTGTGAAACACAAAATTCTAGTTTTGTCTGGAAAAGGAGGAGTTGGCAAGAGCACATTTGCTGCACAGCT
<
<
<
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.acccttacacacgagtccggtgatgtgatcgttcctgaaacttttgcttcttcagACCTTGTAGCGATTGAGGAGCGTATGCGTACTGTGAAACACAAAATTCTAGTTTTGTCTGGAAAAGGAGGAGTTGGCAAGAGCACATTTGCTGCACAGCT
cccttac putative branch site (score: 6)
cttttgcttcttc putative PPT
aaactttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
tttaaagtttgatatttgcttctagtttagcttttagaatttgtgacccttacacacgagtccggtgatgtgatcgttcctgaaacttttgcttcttcagACCTTGTAGCGATTGAGGAGCGTATGCGTACTGTGAAACACAAAATTCTAGTTTTGTCTGGAAAAGGAGGAGTTGGCAAGAGCACATTTGCTGCACAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGCTGC