Sequence
atgc intronic sequence ATGC exonic sequencegtagcgataacaattaatggcaaagttatgtcagctctgtgttcgcaattcgtttttctccacttgtttttaagtttccctgcccatggtctgaatctgtgtttgatccgacttcaatttggttactagAACGCGGCTCTTCTGGACAGCGAGATAATTTATGATCGGGACTTCGATTACGACTACTTCGGCTTCAAGACACTGGAGAGATCATATTTACTGAGAGTGA
Basic information
species | Physcomitrella patens |
transcript | PP1S195_46V6.1 |
intron # | 2 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: PP1S195_46V6.1 (Physcomitrella patens), 3'ss of exon 2
lower sequence: LOC_Os06g07210.1 (Oryza sativa), 3'ss of exon 3
--------------------gtagcgataacaattaatggcaaagttatgtcagctctgt---gttcgcaattcgtttttctccacttgtttttaagtttccctgcccatggtctgaatct----gtgtttgatccgacttcaatttggttactagAACGCGGCTCTTCTGGACAGCGAGATAATTTATGATCGGGACTTCGATTACGACTACTTCGGCTTCAAGACACTGGAGAGATCATATTTACTGAGAGTGA
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gtgagatatcaaattaaactttagggacttgcactgatagctgttcttgttctgatttgtaaaatttactgttccattcaatttattggtcattaggattattgatgtatgttatgcttcttacggtttctgat--gttctgatccttattttcagAATGCTTCTCGCTTGGACAGCGAGATAATTTATGATAGGGACTTCGATTATGATTATTTTGGTTTCAAGACTCTGGAGAGGTCTTACCTCCTGAAACTTG
upper sequence: PP1S195_46V6.1 (Physcomitrella patens), 3'ss of exon 2
lower sequence: GRMZM2G304362_T01 (Zea mays), 3'ss of exon 3
gtagcgataacaattaatggcaaagttatgtcagctctgtgttcgcaattcgtttttctccacttgtttttaagtttccctgcccatggtctgaatctgtgtttgatccgacttcaatttggttactagAACGCGGCTCTTCTGGACAGCGAGATAATTTATGATCGGGACTTCGATTACGACTACTTCGGCTTCAAGACACTGGAGAGATCATATTTACTGAGAGTGA
||| | | | | | ||| | ||| ||| | | || | || || || | | | ||| | | | | || | |||| || |||| ||||||| ||||||||||||||| |||| ||||| ||||||||||| |||||||| || |||||||| || || | ||| |
-------------------acaaggctgt-ttatctc-atacagtaaatctgttgtgccccgcac------aacacaccttgttggaaattgg--ccctcacatgactccaaatgatgttacatttcagAATGCTGCTCGCTTGGACAGTGAGATAATTTATGATAGGGATTTCGACTACGACTACTTTGGCTTCAAAACTCTGGAGAGGTCTTACCTGTTGAAGCTTG
upper sequence: PP1S195_46V6.1 (Physcomitrella patens), 3'ss of exon 2
lower sequence: GRMZM2G340527_T01 (Zea mays), 3'ss of exon 3
------------------------------------------------------------gtagcgataacaattaatggcaaagttatgtcagctctgtgttcgcaattcgtttttctccac------ttgtttttaagtttccctgcccatggtctgaatctgtgtttgatccgacttcaatttggttac----tagAACGCGGCTCTTCTGGACAGCGAGATAATTTATGATCGGGACTTCGATTACGACTACTTCGGCTTCAAGACACTGGAGAGATCATATTTACTGAGAGTGA
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gtgagattctagttgctcctggcacatttctgacagagcatctgtgtagataatgccgatgtgtttctggcagttgaatttactgttgcattcctttttttattaaggttgtttatctcatacagtaaatctgttgtgcccttcactcaccttgatgtaaattggccctcatatcgctccaaatgctgttacatttcagAATGCTGCTCGCTTGGACAGTGAAATAATTTATGATAGGGATTTCGACTATGACTACTTTGGCTTCAAAACTCTGGAGAGGTCTTACCTCTTGAAGCTTGMapped 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|162255799|gb|FC431459.1|FC431459EST: GTTTGAAGTCGCCTCTCATAGATGATGACGTGTACGATCTTATCATCAAG AACGCGGCTCTTCTGGACAGCGAGATAATTTATGATCGGGACTTCGATTAC
genomic: GTTTGAAGTCGCCTCTCATAGATGATGACGTGTACGATCTTATCATCAAGgtagcgataa ... tggttactagAACGCGGCTCTTCTGGACAGCGAGATAATTTATGATCGGGACTTCGATTAC
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tttccctgcccatggtctgaatctgtgtttgatccgacttcaatttggttactagAACGCGGCTCTTCTGGACAGCGAGATAATTTATGATCGGGACTTCGATTACGACTACTTCGGCTTCAAGACACTGGAGAGATCATATTTACTGAGAGTGA
gtttgat putative branch site (score: 5)
ttcaattt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtagcgataacaattaatggcaaagttatgtcagctctgtgttcgcaattcgtttttctccacttgtttttaagtttccctgcccatggtctgaatctgtgtttgatccgacttcaatttggttactagAACGCGGCTCTTCTGGACAGCGAGATAATTTATGATCGGGACTTCGATTACGACTACTTCGGCTTCAAGACACTGGAGAGATCATATTTACTGAGAGTGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGATC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGATCA