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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

ATCAAGAACAACAAGAGATACGCTGGGTCAACTGCTTGGACTGTACAGgtgatttttcaacgtctcgtttcatccttcgatttctggaatggtgtcacagcatctttgtctgaggaacaggggagtgaatgcatcatttcttttggca...

Basic information

species Physcomitrella patens
transcript PP1S29_256V6.1
intron # 5
splice site 5'
intron type U2

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|162171618|gb|FC347559.1|FC347559
EST:     ATCAAGAACAACAAGAGATACGCTGGGTCAACTGCTTGGACTGTACAG                         GAATGTGCCGAAGCCGTGAAAGCTGACTTCGGCTCCATCGACATCCTGGTG
genomic: ATCAAGAACAACAAGAGATACGCTGGGTCAACTGCTTGGACTGTACAGgtgatttttc ... ttttgttaagGAATGTGCCGAAGCCGTGAAAGCTGACTTCGGCTCCATCGACATCCTGGTG
EST: gi|18327390|gb|BJ159392.1|BJ159392
EST:     ATCAAGAACAACAAGAGATACGCTGGGTCAACTGCTTGGACTGTACAG                         GAATGTGCCGAAGCCGTGAAAGCTGACTTCGGCTCCATCGACATCCTGGTG
genomic: ATCAAGAACAACAAGAGATACGCTGGGTCAACTGCTTGGACTGTACAGgtgatttttc ... ttttgttaagGAATGTGCCGAAGCCGTGAAAGCTGACTTCGGCTCCATCGACATCCTGGTG
EST: gi|162182768|gb|FC359515.1|FC359515
EST:     ATCAAGAACAACAAGAGATACGCTGGGTCAACTGCTTGGACTGTACAG                         GAATGTGCCGAAGCCGTGAAAGCTGACTTCGGCTCCATCGACATCCTGGTG
genomic: ATCAAGAACAACAAGAGATACGCTGGGTCAACTGCTTGGACTGTACAGgtgatttttc ... ttttgttaagGAATGTGCCGAAGCCGTGAAAGCTGACTTCGGCTCCATCGACATCCTGGTG
EST: gi|19777824|gb|BQ039232.1|BQ039232
EST:     ATCAAGAACAACAAGAGATACGCTGGGTCAACTGCTTGGACTGTACAG                         GAATGTGCCGAAGCCGTGAAAGCTGACTTCGGCTCCATCGACATCCTGGTG
genomic: ATCAAGAACAACAAGAGATACGCTGGGTCAACTGCTTGGACTGTACAGgtgatttttc ... ttttgttaagGAATGTGCCGAAGCCGTGAAAGCTGACTTCGGCTCCATCGACATCCTGGTG
EST: gi|67719586|gb|BJ969845.1|BJ969845
EST:     ATCAAGAACAACAAGAGATACGCTGGGTCAACTGCTTGGACTGTACAG                         GAATGTGCCGAAG
genomic: ATCAAGAACAACAAGAGATACGCTGGGTCAACTGCTTGGACTGTACAGgtgatttttc ... ttttgttaagGAATGTGCCGAAG
EST: gi|67718262|gb|BJ968521.1|BJ968521
EST:     ATCAAGAACAACAAGAGATACGCTGGGTCAACTGCTTGGACTGTACAG                         GAATGTGCCGAAGCCGTGAAAGCTGACTTCGGCTCCATCGACATCCTGGTG
genomic: ATCAAGAACAACAAGAGATACGCTGGGTCAACTGCTTGGACTGTACAGgtgatttttc ... ttttgttaagGAATGTGCCGAAGCCGTGAAAGCTGACTTCGGCTCCATCGACATCCTGGTG
EST: gi|162176349|gb|FC353534.1|FC353534
EST:     ATCAAGAACAACAAGAGATACGCTGGGTCAACTGCTTGGACTGTACAG                         GAATGTGCCGAAGCCGTGAAAGCTGACTTCGGCTCCATCGACATCCTGGTG
genomic: ATCAAGAACAACAAGAGATACGCTGGGTCAACTGCTTGGACTGTACAGgtgatttttc ... ttttgttaagGAATGTGCCGAAGCCGTGAAAGCTGACTTCGGCTCCATCGACATCCTGGTG
EST: gi|208359693|gb|DC930283.1|DC930283
EST:     ATCAAGAACAACAAGAGATACGCTGGGTCAACTGCTTGGACTGTACAG                         GAATGTGCCGAANCCGTGAAANCTGACTTCGGCTC-ATCGACATCCTGGTG
genomic: ATCAAGAACAACAAGAGATACGCTGGGTCAACTGCTTGGACTGTACAGgtgatttttc ... ttttgttaagGAATGTGCCGAAGCCGTGAAAGCTGACTTCGGCTCCATCGACATCCTGGTG
EST: gi|162167232|gb|FC342797.1|FC342797
EST:     ATCAAGAACAACAAGAGATACGCTGGGTCAACTGCTTGGACTGTACAG                         GAATGTGCCGAAGCCGTGAAAGCTGACTTCGGCTCCATCGACATCCTGGTG
genomic: ATCAAGAACAACAAGAGATACGCTGGGTCAACTGCTTGGACTGTACAGgtgatttttc ... ttttgttaagGAATGTGCCGAAGCCGTGAAAGCTGACTTCGGCTCCATCGACATCCTGGTG
EST: gi|19789330|gb|BQ041244.1|BQ041244
EST:     ATCAAGAACAACAAGAGATACGCTGGGTCAACTGCTTGGACTGTACAG                         GAATGTGCCGAAGCCGTGAAAGCTGACTTCGGCTCCATCGACATCCTGGTG
genomic: ATCAAGAACAACAAGAGATACGCTGGGTCAACTGCTTGGACTGTACAGgtgatttttc ... ttttgttaagGAATGTGCCGAAGCCGTGAAAGCTGACTTCGGCTCCATCGACATCCTGGTG
EST: gi|162169758|gb|FC345295.1|FC345295
EST:     ATCAAGAACAACAAGAGATACGCTGGGTCAACTGCTTGGACTGTACAG                         GAATGTGCCGAAGCCGTGAAAGCTGACTTCGGCTCCATCGACATCCTGGTG
genomic: ATCAAGAACAACAAGAGATACGCTGGGTCAACTGCTTGGACTGTACAGgtgatttttc ... ttttgttaagGAATGTGCCGAAGCCGTGAAAGCTGACTTCGGCTCCATCGACATCCTGGTG
EST: gi|162176594|gb|FC353063.1|FC353063
EST:     ATCAAGAACAACAAGAGATACGCTGGGTCAACTGCTTGGACTGTACAG                         GAATGTGCCGAAGCCGTGAAAGCTGACTTCGGCTCCATCGACATCCTGGTG
genomic: ATCAAGAACAACAAGAGATACGCTGGGTCAACTGCTTGGACTGTACAGgtgatttttc ... ttttgttaagGAATGTGCCGAAGCCGTGAAAGCTGACTTCGGCTCCATCGACATCCTGGTG
EST: gi|162181164|gb|FC357609.1|FC357609
EST:     ATCAAGAACAACAAGAGATACGCTGGGTCAACTGCTTGGACTGTACAG                         GAATGTGCCGAAGCCGTGAAAGCTGACTTCGGCTCCATCGACATCCTGGTG
genomic: ATCAAGAACAACAAGAGATACGCTGGGTCAACTGCTTGGACTGTACAGgtgatttttc ... ttttgttaagGAATGTGCCGAAGCCGTGAAAGCTGACTTCGGCTCCATCGACATCCTGGTG
EST: gi|67718833|gb|BJ969092.1|BJ969092
EST:     ATCAAGAACAACAAGAGATACGCTGGGTCAACTGCTTGGACTGTACAG                         GAATGTGCCGAAGCCGTGAAAGCTGACTTCGGCTCCATCGACATCCTGGTG
genomic: ATCAAGAACAACAAGAGATACGCTGGGTCAACTGCTTGGACTGTACAGgtgatttttc ... ttttgttaagGAATGTGCCGAAGCCGTGAAAGCTGACTTCGGCTCCATCGACATCCTGGTG
EST: gi|100384688|gb|BY950678.1|BY950678
EST:     ATCAAGAACAACAAGAGATACGCTGGGTCAACTGCTTGGACTGTACAG                         GAATGTGCCGAAGCCGTGAAAGCTGACTTTCG-CTCCATCGACATCCTGGT
genomic: ATCAAGAACAACAAGAGATACGCTGGGTCAACTGCTTGGACTGTACAGgtgatttttc ... ttttgttaagGAATGTGCCGAAGCCGTGAAAGCTGACTT-CGGCTCCATCGACATCCTGGT
EST: gi|100429370|gb|BY978077.1|BY978077
EST:     ATCAAGAACAACAAGAGATACGCTGGGTGCA-CTGCTTGGACTGTACAG                         GAAATGTGCCGAAGCCGTGAAAGCTGACTTCGGCTCC
genomic: ATCAAGAACAACAAGAGATACGCTGGGT-CAACTGCTTGGACTGTACAGgtgatttttc ... ttttgttaagGAA-TGTGCCGAAGCCGTGAAAGCTGACTTCGGCTCC
EST: gi|100403476|gb|BY991219.1|BY991219
EST:     ATCAAGAACAACAAGAGATACGCTGGGTCAACTGCTTGGACTGTACAG                         GAATGTGCCGAAGCCGTGAAAGCTGACTTCGGCTCCATCGACATCCTGGTG
genomic: ATCAAGAACAACAAGAGATACGCTGGGTCAACTGCTTGGACTGTACAGgtgatttttc ... ttttgttaagGAATGTGCCGAAGCCGTGAAAGCTGACTTCGGCTCCATCGACATCCTGGTG
EST: gi|162241271|gb|FC416902.1|FC416902
EST:     ATCAAGAACAACAAGAGATACGCTGGGTCAACTGCTTGGACTGTACAG                         GAATGTGCCGAAGCCGTGAAAGCTGACTTCGGCTCCATCGACATCCTGGTG
genomic: ATCAAGAACAACAAGAGATACGCTGGGTCAACTGCTTGGACTGTACAGgtgatttttc ... ttttgttaagGAATGTGCCGAAGCCGTGAAAGCTGACTTCGGCTCCATCGACATCCTGGTG

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: 34 (upstream exon), 33 (downstream exon)
Score: 8

ATCAAGAACAACAAGAGATACGCTGGGTCAACTGCTTGGACTGTACAGgtgatttttc ... ttttgttaagGAATGTGCCGAAGCCGTGAAAGCTGACTTCGGCTCCATCGACATCCTGGTGCATTCACTTGCTAATGGGCCTGAA




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ATCAAGAACAACAAGAGATACGCTGGGTCAACTGCTTGGACTGTACAGgtgatttttcaacgtctcgtttcatccttcgatttctggaatggtgtcacagcatctttgtctgaggaacaggggagtgaatgcatcatttcttttggca

-  AAGAAC
- - - - - - AAGAGA