Sequence
atgc intronic sequence ATGC exonic sequencegtacatttatctcatcatcgatgctcaggttacataggacacatactaatcatttagtgtatgccaagagtcggtcgacctgcggctgacattgctggtggttacattgcagGTTGGACCGAGACTACCCAAGGATCGCGAGAGATTTCCTCCCAACAACATGCTGCTTGTGCTTACAGGTGCAGGGCTGTTATGGCTGGGGTGGTCAGGTT
Basic information
species | Physcomitrella patens |
transcript | PP1S120_140V6.1 |
intron # | 1 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: PP1S120_140V6.1 (Physcomitrella patens), 3'ss of exon 1
lower sequence: LOC_Os02g34580.1 (Oryza sativa), 3'ss of exon 2
gtacatttatctcatcatcgatgctcaggttacataggacacatactaatcatttagtgtatgccaagagtcggtcgacctgcggctgacattgctggtggtt---acattgcagGTTGGACCGAGACTACCCAAGGATCGCGAGAGATTTCCTCCCAACAACATGCTGCTTGTGCTTACAGGTGCAGGGCTGTTATGGCTGGGGTGGTCAGGTT
|| | || | | || | | || | | | | |||| || ||| ||| | || ||||||||||||| || | | ||| | |||||||| || ||||||||||| ||||| ||||| |||| || |||||| | ||||| |||||| ||||||
---------------------------------gtacggcaaagatctctctctggttaaattcaccatgccactt---ctgcatctatgatttctgacatctcgcaccatgcagGTTGGACCAAGGTCAGCATCAGATAGGGAGAGATTCCCGCCCAACAACATACTGCTGGTGCTAGCAGGGGCGGGGCTGCTGTGGCTTGGGTGGACAGGTTMapped 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|19778171|gb|BQ039268.1|BQ039268EST: ACGTAATCCATGTCTCCTCCGGCGCTGCTGGTTTCGTTGCGGCCTACTGG GTTGGACCGAGACTACCCAAGGATCGCGAGAGATTTCCTCCCAACAACATG
genomic: ACGTAATCCATGTCTCCTCCGGCGCTGCTGGTTTCGTTGCGGCCTACTGGgtacatttat ... tacattgcagGTTGGACCGAGACTACCCAAGGATCGCGAGAGATTTCCTCCCAACAACATG
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tgtatgccaagagtcggtcgacctgcggctgacattgctggtggttacattgcagGTTGGACCGAGACTACCCAAGGATCGCGAGAGATTTCCTCCCAACAACATGCTGCTTGTGCTTACAGGTGCAGGGCTGTTATGGCTGGGGTGGTCAGGTT
ggctgac putative branch site (score: 3)
ttacatt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtacatttatctcatcatcgatgctcaggttacataggacacatactaatcatttagtgtatgccaagagtcggtcgacctgcggctgacattgctggtggttacattgcagGTTGGACCGAGACTACCCAAGGATCGCGAGAGATTTCCTCCCAACAACATGCTGCTTGTGCTTACAGGTGCAGGGCTGTTATGGCTGGGGTGGTCAGGTT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGTT