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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ggcttgtagactcattgttccttgttgagattctttttaactggatctgttagcttcacatgattgatggataacatgaacatcgtttggaaccgctcagGATGCCTTGTCGTCAAAGGGCCTCGTTCCCTTACTTGGAATTGATGTCTGGGAACATGCCTACTACTTGCAG

Basic information

species Physcomitrella patens
transcript PP1S174_60V6.1
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S174_60V6.1 (Physcomitrella patens), 3'ss of exon 4
lower sequence: GRMZM2G059991_T01 (Zea mays), 3'ss of exon 4
---------ggcttgtagactcattgttccttg-ttgagattctttttaactggatctgttagcttcacatgattgatggataacatgaacatcgtttggaaccgctcagGATGCCTTGTCGTCAAAGGGCCTCGTTCCCTTACTTGGAATTGATGTCTGGGAACATGCCTACTACTTGCAG
         ||  || ||    || | |  | | |||    ||| |  |  | |  | |   | |   |   |   |  | |||  | |  ||| |   | | | ||| || || ||    ||  |||  | | |||||  |  | || |||||||||||||||||||| |||||| |||||
ataaaaaagggtgtgaagggaaatggatgttgggttgcttatctgtgaagattgtacagaaggttgttccatacacacagctaattttagtatcttgcagGATC-CTCTGG-TGACTAAAGGTGCAAG--CTTGGTTCCGCTGTTGGGGATTGATGTCTGGGAACATGCATACTACCTGCAG
















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|162260962|gb|FC438019.1|FC438019
EST:     GTTTGAACAAGGATTTGAAGAGACTTGAAGTGCAGACAACCATGAACCAG                         GATGCCTTGTCGTCAAAGGGCCTCGTTCCCTTACTTGGAATTGATGTCTGG
genomic: GTTTGAACAAGGATTTGAAGAGACTTGAAGTGCAGACAACCATGAACCAGgtttgtgagg ... aaccgctcagGATGCCTTGTCGTCAAAGGGCCTCGTTCCCTTACTTGGAATTGATGTCTGG
EST: gi|208366209|gb|DC955308.1|DC955308
EST:     GTTTGAACAAGGATTTGAAGAGACTTGAAGTGCAGACAACCATGAACCAG                         GATGCCTTGTCGTCAAAGGGCCTCGTTCCCTTACTTGGAATTGATGTCTGG
genomic: GTTTGAACAAGGATTTGAAGAGACTTGAAGTGCAGACAACCATGAACCAGgtttgtgagg ... aaccgctcagGATGCCTTGTCGTCAAAGGGCCTCGTTCCCTTACTTGGAATTGATGTCTGG
EST: gi|162235362|gb|FC412329.1|FC412329
EST:     GTTTGAACAAGGATTTGAAGAGACTTGAAGTGCAGACAACCATGAACCAG                         GATGCCTTGTCGTCAAAGGGCCTCGTTCCCTTACTTGGAATTGATGTCTGG
genomic: GTTTGAACAAGGATTTGAAGAGACTTGAAGTGCAGACAACCATGAACCAGgtttgtgagg ... aaccgctcagGATGCCTTGTCGTCAAAGGGCCTCGTTCCCTTACTTGGAATTGATGTCTGG
EST: gi|208391751|gb|DC942313.1|DC942313
EST:     GTTTGAACAAGGATTTGAAGAGACTTGAAGTGCAGACAACCATGAACCAG                         GATGCCTTGTCGTCAAAGGGCCTCGTTCCCTTACTTGGAATTGATGTCTGG
genomic: GTTTGAACAAGGATTTGAAGAGACTTGAAGTGCAGACAACCATGAACCAGgtttgtgagg ... aaccgctcagGATGCCTTGTCGTCAAAGGGCCTCGTTCCCTTACTTGGAATTGATGTCTGG
EST: gi|208397933|gb|DC916688.1|DC916688
EST:     GTTTGAACAAGGATTTGAAGAGACTTGAAGTGCAGACAACCATGAACCAG                         GATGCCTTGTCGTCAAAGGGCCTCGTTCCCTTACTTGGAATTGATGTCTGG
genomic: GTTTGAACAAGGATTTGAAGAGACTTGAAGTGCAGACAACCATGAACCAGgtttgtgagg ... aaccgctcagGATGCCTTGTCGTCAAAGGGCCTCGTTCCCTTACTTGGAATTGATGTCTGG
EST: gi|208348700|gb|DC926375.1|DC926375
EST:     GTTTGAACAAGGATTTGAAGAGACTTGAAGTGCAGACAACCATGAACCAG                         GATGCCTTGTCGTCAAAGGGCCTCGTTCCCTTACTTGGAATTGATGTCTGG
genomic: GTTTGAACAAGGATTTGAAGAGACTTGAAGTGCAGACAACCATGAACCAGgtttgtgagg ... aaccgctcagGATGCCTTGTCGTCAAAGGGCCTCGTTCCCTTACTTGGAATTGATGTCTGG
EST: gi|208344646|gb|DC912592.1|DC912592
EST:     GTTTGAACAAGGATTTGAAGAGACTTGAAGTGCAGACAACCATGAACCAG                         GATGCCTTGTCGTCAAAGGGCCTCGTTCCCTTACTTGGAATTGATGTCTGG
genomic: GTTTGAACAAGGATTTGAAGAGACTTGAAGTGCAGACAACCATGAACCAGgtttgtgagg ... aaccgctcagGATGCCTTGTCGTCAAAGGGCCTCGTTCCCTTACTTGGAATTGATGTCTGG
EST: gi|19789071|gb|BQ041074.1|BQ041074
EST:     GTTTGAACAAGGATTTGAAGAGACTTGAAGTGCAGACAACCATGAACCAG                         GATGCCTTGTCGTCAAAGGGCCTCGTTCCCTTACTTGGAATTGATGTCTGG
genomic: GTTTGAACAAGGATTTGAAGAGACTTGAAGTGCAGACAACCATGAACCAGgtttgtgagg ... aaccgctcagGATGCCTTGTCGTCAAAGGGCCTCGTTCCCTTACTTGGAATTGATGTCTGG
EST: gi|37834392|gb|BJ592404.1|BJ592404
EST:     GTTTGAACAAGGATTTGAAGAGACTTGAAGTGCAGACAACCATGAACCAG                         GATGCCTTGTCGTCAAAGGGCCTCGTTCCCTTACTTGGAATTGATGTCTGG
genomic: GTTTGAACAAGGATTTGAAGAGACTTGAAGTGCAGACAACCATGAACCAGgtttgtgagg ... aaccgctcagGATGCCTTGTCGTCAAAGGGCCTCGTTCCCTTACTTGGAATTGATGTCTGG
EST: gi|67570006|gb|BJ942830.1|BJ942830
EST:     GTTTGAACAAGGATTTGAAGAGACTTGAAGTGCAGACAACCATGAACCAG                         GATGCCTTGTCGTCAAAGGGCCTCGTTCCCTTACTTGGAATTGATGTCTGG
genomic: GTTTGAACAAGGATTTGAAGAGACTTGAAGTGCAGACAACCATGAACCAGgtttgtgagg ... aaccgctcagGATGCCTTGTCGTCAAAGGGCCTCGTTCCCTTACTTGGAATTGATGTCTGG
EST: gi|37831305|gb|BJ589317.1|BJ589317
EST:     GTTTGAACAAGGATTTGAAGAGACTTGAAGTGCAGACAACCATGAACCAG                         GATGCCTTGTCGTCAAAGGGCCTCGTTCCCTTACTTGGAATTGATGTCTGG
genomic: GTTTGAACAAGGATTTGAAGAGACTTGAAGTGCAGACAACCATGAACCAGgtttgtgagg ... aaccgctcagGATGCCTTGTCGTCAAAGGGCCTCGTTCCCTTACTTGGAATTGATGTCTGG
EST: gi|67693275|gb|BJ953508.1|BJ953508
EST:     GTTTGAACAAGGATTTGAAGAGACTTGAAGTGCAGACAACCATGAACCAG                         GATGCCTTGTCGTCAAAGGGCCTCGTTCCCTTACTTGGAATTGATGTCTGG
genomic: GTTTGAACAAGGATTTGAAGAGACTTGAAGTGCAGACAACCATGAACCAGgtttgtgagg ... aaccgctcagGATGCCTTGTCGTCAAAGGGCCTCGTTCCCTTACTTGGAATTGATGTCTGG
EST: gi|100441642|gb|BY962733.1|BY962733
EST:     GTTTGAACAAGGATTTGAAGAGACTTGAAGTGCAGACAACCATGAACCAG                         GATGCTTTGTCGTCAAAGGGCCTCG
genomic: GTTTGAACAAGGATTTGAAGAGACTTGAAGTGCAGACAACCATGAACCAGgtttgtgagg ... aaccgctcagGATGCCTTGTCGTCAAAGGGCCTCG
EST: gi|208377497|gb|DC902792.1|DC902792
EST:     GTTTGAACAAGGATTTGAANANACTTGAANTGCANACAACCATGAACCAN                         GATGCCTTGTCGTCAAAGG-CCTCGTTCC
genomic: GTTTGAACAAGGATTTGAAGAGACTTGAAGTGCAGACAACCATGAACCAGgtttgtgagg ... aaccgctcagGATGCCTTGTCGTCAAAGGGCCTCGTTCC
EST: gi|162235361|gb|FC412328.1|FC412328
EST:     GTTTGAACAAGGATTTGAAGAGACTTGAAGTGCAGACAACCATGAACCAG                         GATGCCTTGTCGTCAAAGGGCCTCGTTCCCTTACTTGGAATTGATGTCTGG
genomic: GTTTGAACAAGGATTTGAAGAGACTTGAAGTGCAGACAACCATGAACCAGgtttgtgagg ... aaccgctcagGATGCCTTGTCGTCAAAGGGCCTCGTTCCCTTACTTGGAATTGATGTCTGG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tctgttagcttcacatgattgatggataacatgaacatcgtttggaaccgctcagGATGCCTTGTCGTCAAAGGGCCTCGTTCCCTTACTTGGAATTGATGTCTGGGAACATGCCTACTACTTGCAG
                       ggataac  putative branch site (score: 3)
                         ataacat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ggcttgtagactcattgttccttgttgagattctttttaactggatctgttagcttcacatgattgatggataacatgaacatcgtttggaaccgctcagGATGCCTTGTCGTCAAAGGGCCTCGTTCCCTTACTTGGAATTGATGTCTGGGAACATGCCTACTACTTGCAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - cacatga