Sequence
atgc intronic sequence ATGC exonic sequence...tctcgtcatcgagggaaccggagtgtttgtggacgaggccggtgctggcaagcacatccaggctggagccaagaaggtattgatcaccgctccaggcaagGGTCCCATCCCTACCTACGTGGTGGGAGTGAATGAGCAAGACTACAAGCACTCTGACACCATCATCAGCAACGCCTCCTGCACCACCAACTGCTTGGCAC
Basic information
species | Physcomitrella patens |
transcript | PP1S86_156V6.2 |
intron # | 3 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: PP1S86_156V6.2 (Physcomitrella patens), 3'ss of exon 3
lower sequence: AT1G12900.3 (Arabidopsis thaliana), 3'ss of exon 3
tctcgtcatcgagggaaccggagtgtttgtggacgaggccggtgctggcaagcacatccaggctggagccaagaaggtattgatcaccgctccaggcaagGGTCCCATCCCTACCTACGTGGTGGGAGTGAATGAGCAAGACTACAAGCACTCTGACACCATCATCAGCAACGCCTCCTGCACCACCAACTGCTTGGCAC
| | | | || | | | | || || | || | | | || | | | | ||||| | | || | | | |||||| || | || | || || | || | |||| || || | | | | ||| |
---------gtaagttaaaacaacacttctcatatcatttgaattgaatcaacccagttagatctaaacctggt-gatgatgtttagGGAACTAGGCATTGACTTAGT---TATCGAAGGAACCGGAGTGTTTGTTGACAGAGACG-GTGCTGGGA-AGCACCTTCAGG-----CTGGAGC-CAAGAAGGTTCTTATC--
upper sequence: PP1S86_156V6.2 (Physcomitrella patens), 3'ss of exon 3
lower sequence: AT1G12900.2 (Arabidopsis thaliana), 3'ss of exon 3
tctcgtcatcgagggaaccggagtgtt-tgtggacgaggccggtgctggcaagcacat-ccaggctggagccaagaaggtattgatcaccgctccaggcaagGGTCCCATCCCTACCTACGTGGTGGGAGTGAATGAGCAAGACTACAAGCACTCTGACACCATCATCAGCAACGCCTCCTGCACCACCAACTGCTTGGCAC
|| | | | | | || | | | | | | || || | || | | || | || | | | || | || || || || | || | |||||| | | | || || | |
----gttaaaacaacacttctcatatcatttgaattgaatcaacccagttagatctaaacctggtgatgatgtttagGGAACTAGGCATTGACTTAGTTATCGAAGGAA--CCGGAGTGTTTGTTGACAGAGACGGTGCTGGG----AAGCACCTTCAGGCTGGAGCCAAGAAGGTTCTTATC-------------------
upper sequence: PP1S86_156V6.2 (Physcomitrella patens), 3'ss of exon 3
lower sequence: AT3G26650.1 (Arabidopsis thaliana), 3'ss of exon 3
--------tctcgtcatcgagggaaccggagtgtttgtggacgaggccggtgctggcaagcacatcca----ggctggagcc--aagaaggtattgatcaccgctccaggcaagGGTCCCATCCCTACCTACGTGGTGGGAGTGAATGAGCAAGACTACAAGCACTCTGACACCATCATCAGCAACGCCTCCTGCACCACCAACTGCTTGGCAC
|| | | | | | | ||| | | || | | ||| || || ||| | | | || || || | | | | || || | || | || ||| | ||| | || ||| ||| | || || | |
gtaagtcgaaaaaccacttatgtgatcagtctttttatct-caagtctagaataagcatttgaattggatatggttggtatcttagGGAGCTAGGAATTGACATTGTCATCGAAGGAACCG-----GAGTGTTTGTGGATAGAGAAGGTGCAGGG----AAACACATTGAAGCTGGTGCCAAGAAGGTTATCATT-------------------
upper sequence: PP1S86_156V6.2 (Physcomitrella patens), 3'ss of exon 3
lower sequence: Vv14s0068g00680.t01 (Vitis vinifera), 3'ss of exon 3
--tctcgtcatcgagggaaccggagtgtttgtggacgaggccggt--gctggcaagcacatccaggctggagccaagaaggtattgatcac-cgctccaggcaagGGTCCCATCCCTACCTACGTGGTGGGAGTGAATGAGCAAGACTACAAGCACTC-TGACACCATCATCAGCAACGCCTCCTGCACCACCAAC-TGCTTGGCAC
| | | | ||| |||| | | ||| ||||| || ||| | | || || | || | |||||| | | | | ||| ||| | | || | | | | | || || | || || | | | ||| || |||| |
gtaactaatactaatcacccatcaagttttttggatcgaatggactaattagcattcacattcataatggtg-----atggcttttgttacatggtccagG---GACTTGGACATTGATCTA-GTGATAGAAG-GGACAGGGGTGTTTGTGGACAGAGATGGTGCAGGCAAGCACATCCAGGCAGGGGCCAAGAAGGTGCTCATC--Mapped 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|100388525|gb|BY952127.1|BY952127EST: ATGCCGATGTTAAGGTGGAGGGCAATGACGCCATCAGCGTGGACGGCAAG GGTCCCATCCCTACCTACGTGGTGGGAGTGAATGAGCAAGACTACAAGCAC
genomic: ATGCCGATGTTAAGGTGGAGGGCAATGACGCCATCAGCGTGGACGGCAAGgtcatcaagg ... tccaggcaagGGTCCCATCCCTACCTACGTGGTGGGAGTGAATGAGCAAGACTACAAGCAC
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tggcaagcacatccaggctggagccaagaaggtattgatcaccgctccaggcaagGGTCCCATCCCTACCTACGTGGTGGGAGTGAATGAGCAAGACTACAAGCACTCTGACACCATCATCAGCAACGCCTCCTGCACCACCAACTGCTTGGCAC
tattgat putative branch site (score: 3)
ccgctcc putative PPT
tattgat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
tctcgtcatcgagggaaccggagtgtttgtggacgaggccggtgctggcaagcacatccaggctggagccaagaaggtattgatcaccgctccaggcaagGGTCCCATCCCTACCTACGTGGTGGGAGTGAATGAGCAAGACTACAAGCACTCTGACACCATCATCAGCAACGCCTCCTGCACCACCAACTGCTTGGCAC
- - - - - - - - - - - - - - - - - - - - - - - - - - cacatcc