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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gttaatattcctacttacgggtttcttgcttagcaattgaaacccaccccgatcttctcctaaattgcaaattgctttaaaatcgttcgtgctctcttaacacgttctgtctggtgtaccattcgcagATTGAAGGGTATCCTACCATTCTCTTCTTCCCAGCAGGAGACAAGAGCGTTGAGCCT

Basic information

species Physcomitrella patens
transcript PP1S422_7V6.1
intron # 6
splice site 3'
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|162166449|gb|FC342431.1|FC342431
EST:     TCGTGATTGCAAAGATGGATGGCACCAAAAACGAGCACGAACGTCTCAAG                         ATTGAAGGGTATCCTACCATTCTCTTCTTCCCAGCAGGAGACAAGAGCGTT
genomic: TCGTGATTGCAAAGATGGATGGCACCAAAAACGAGCACGAACGTCTCAAGgttaatattc ... ccattcgcagATTGAAGGGTATCCTACCATTCTCTTCTTCCCAGCAGGAGACAAGAGCGTT
EST: gi|162262522|gb|FC439734.1|FC439734
EST:     TCGTGATTGCAAAGATGGATGGCACCAAAAACGAGCACGAACGTCTCAAG                         ATTGAAGGGTATCCTACCATTCTCTTCTTCCCAGCAGGAGACAAGAGCGTT
genomic: TCGTGATTGCAAAGATGGATGGCACCAAAAACGAGCACGAACGTCTCAAGgttaatattc ... ccattcgcagATTGAAGGGTATCCTACCATTCTCTTCTTCCCAGCAGGAGACAAGAGCGTT
EST: gi|37840233|gb|BJ598241.1|BJ598241
EST:     TCGTGATTGCAAAGATGGATGGCACCAAAAACGAGCACGAACGTCTCAAG                         ATTGAAGGGTATCCTACCATTCTCTTCTTCCCAGCAGGAGACAAGAGCGTT
genomic: TCGTGATTGCAAAGATGGATGGCACCAAAAACGAGCACGAACGTCTCAAGgttaatattc ... ccattcgcagATTGAAGGGTATCCTACCATTCTCTTCTTCCCAGCAGGAGACAAGAGCGTT
EST: gi|18334128|gb|BJ166144.1|BJ166144
EST:     AAAACGAGCACGAACGTCTCAAG                         ATTGAAGGGTATCCTACCATTCTCTTCTTCCCAGCAGGAGACAAGAGCGTT
genomic: AAAACGAGCACGAACGTCTCAAGgttaatattc ... ccattcgcagATTGAAGGGTATCCTACCATTCTCTTCTTCCCAGCAGGAGACAAGAGCGTT
EST: gi|162171847|gb|FC348984.1|FC348984
EST:     TCGTGATTGCAAAGATGGATGGCACCAAAAACGAGCACGAACGTCTCAAG                         ATTGAAGGGTATCCTACCATTCTCTTCTTCCCAGCAGGAGACAAGAGCGTT
genomic: TCGTGATTGCAAAGATGGATGGCACCAAAAACGAGCACGAACGTCTCAAGgttaatattc ... ccattcgcagATTGAAGGGTATCCTACCATTCTCTTCTTCCCAGCAGGAGACAAGAGCGTT
EST: gi|18336444|gb|BJ168466.1|BJ168466
EST:     TCGTGATTGCAAAGATGGATGGCACCAAAAACGAGCACGAACGTCTCAAG                         ATTGAAGGGTATCCTACCATTCTCTTCTTCCCAGCAGGAGACAAGAGCGTT
genomic: TCGTGATTGCAAAGATGGATGGCACCAAAAACGAGCACGAACGTCTCAAGgttaatattc ... ccattcgcagATTGAAGGGTATCCTACCATTCTCTTCTTCCCAGCAGGAGACAAGAGCGTT
EST: gi|37827445|gb|BJ585457.1|BJ585457
EST:     TCGTGATTGCAAAGATGGATGGCACCAAAAACGAGCACGAACGTCTCAAG                         ATTGAAGGGTATCCTACCATTCTCTTCTTCCCAGCAGGAGACAAGAGCGTT
genomic: TCGTGATTGCAAAGATGGATGGCACCAAAAACGAGCACGAACGTCTCAAGgttaatattc ... ccattcgcagATTGAAGGGTATCCTACCATTCTCTTCTTCCCAGCAGGAGACAAGAGCGTT
EST: gi|67720293|gb|BJ970552.1|BJ970552
EST:     TCGTGATTGCAAAGATGGATGGCACCAAAAACGAGCACGAACGTCTCAAG                         ATTGAAGGGTATCCTACCATTCTCTTCTTCCCAGCAGGAGACAAGAGCGTT
genomic: TCGTGATTGCAAAGATGGATGGCACCAAAAACGAGCACGAACGTCTCAAGgttaatattc ... ccattcgcagATTGAAGGGTATCCTACCATTCTCTTCTTCCCAGCAGGAGACAAGAGCGTT
EST: gi|162185363|gb|FC360937.1|FC360937
EST:     TCGTGATTGCAAAGATGGATGGCACCAAAAACGAGCACGAACGTCTCAAG                         ATTGAAGGGTATCCTACCATTCTCTTCTTCCCAGCAGGAGACAAGAGCGTT
genomic: TCGTGATTGCAAAGATGGATGGCACCAAAAACGAGCACGAACGTCTCAAGgttaatattc ... ccattcgcagATTGAAGGGTATCCTACCATTCTCTTCTTCCCAGCAGGAGACAAGAGCGTT
EST: gi|37853537|gb|BJ611545.1|BJ611545
EST:     TCGTGATTGCAAAGATGGATGGCACCAAAAACGAGCACGAACGTCTCAAG                         ATTGAAGGGTATCCTACCATTCTCTTCTTCCCAGCAGGAGACAAGAGCGTT
genomic: TCGTGATTGCAAAGATGGATGGCACCAAAAACGAGCACGAACGTCTCAAGgttaatattc ... ccattcgcagATTGAAGGGTATCCTACCATTCTCTTCTTCCCAGCAGGAGACAAGAGCGTT
EST: gi|37827885|gb|BJ585897.1|BJ585897
EST:     ACGAGCACGAACGTCTCAAG                         ATTGAAGGGTATCCTACCATTCTCTTCTTCCCAGCAGGAGACAAGAGCGTT
genomic: ACGAGCACGAACGTCTCAAGgttaatattc ... ccattcgcagATTGAAGGGTATCCTACCATTCTCTTCTTCCCAGCAGGAGACAAGAGCGTT
EST: gi|162248896|gb|FC422890.1|FC422890
EST:     TCGTGATTGCAAAGATGGATGGCACCAAAAACGAGCACGAACGTCTCAAG                         ATTGAAGGGTATCCTACCATTCTCTTCTTCCCAGCAGGAGACAAGAGCGTT
genomic: TCGTGATTGCAAAGATGGATGGCACCAAAAACGAGCACGAACGTCTCAAGgttaatattc ... ccattcgcagATTGAAGGGTATCCTACCATTCTCTTCTTCCCAGCAGGAGACAAGAGCGTT
EST: gi|162248487|gb|FC420934.1|FC420934
EST:     TCGTGATTGCAAAGATGGATGGCACCAAAAACGAGCACGAACGTCTCAAG                         ATTGAAGGGTATCCTACCATTCTCTTCTTCCCAGCAGGAGACAAGAGCGTT
genomic: TCGTGATTGCAAAGATGGATGGCACCAAAAACGAGCACGAACGTCTCAAGgttaatattc ... ccattcgcagATTGAAGGGTATCCTACCATTCTCTTCTTCCCAGCAGGAGACAAGAGCGTT
EST: gi|208377612|gb|DC926894.1|DC926894
EST:     TCGTGATTGCAAAGATGGATGGCACCAAAAACGAGCACGAACGTCTCAAG                         ATTGAAGGGTATCCTACCATTCTCTTCTTCCCAGCAGGAGACAAGAGCGTT
genomic: TCGTGATTGCAAAGATGGATGGCACCAAAAACGAGCACGAACGTCTCAAGgttaatattc ... ccattcgcagATTGAAGGGTATCCTACCATTCTCTTCTTCCCAGCAGGAGACAAGAGCGTT
EST: gi|162254391|gb|FC430526.1|FC430526
EST:     TCGTGATTGCAAAGATGGATGGCACCAAAAACGAGCACGAACGTCTCAAG                         ATTGAAGGGTATCCTACCATTCTCTTCTTCCCAGCAGGAGACAAGAGCGTT
genomic: TCGTGATTGCAAAGATGGATGGCACCAAAAACGAGCACGAACGTCTCAAGgttaatattc ... ccattcgcagATTGAAGGGTATCCTACCATTCTCTTCTTCCCAGCAGGAGACAAGAGCGTT
EST: gi|37844797|gb|BJ602805.1|BJ602805
EST:     TCGTGATTGCAAAGATGGATGGCACCAAAAACGAGCACGAACGTCTCAAG                         ATTGAAGGGTATCCTACCATTCTCTTCTTCCCAGCAGGAGACAAGAGCGTT
genomic: TCGTGATTGCAAAGATGGATGGCACCAAAAACGAGCACGAACGTCTCAAGgttaatattc ... ccattcgcagATTGAAGGGTATCCTACCATTCTCTTCTTCCCAGCAGGAGACAAGAGCGTT
EST: gi|67694073|gb|BJ954306.1|BJ954306
EST:     TCGTGATTGCAAAGATGGATGGCACCAAAAACGAGCACGAACGTCTCAAG                         ATTGAAGGGTATCCTACCATTCTCTTCTTCCCAGCAGGAGACAAGAGCGTT
genomic: TCGTGATTGCAAAGATGGATGGCACCAAAAACGAGCACGAACGTCTCAAGgttaatattc ... ccattcgcagATTGAAGGGTATCCTACCATTCTCTTCTTCCCAGCAGGAGACAAGAGCGTT
EST: gi|208378241|gb|DC918862.1|DC918862
EST:     TCGTGATTGCAAAGATGGATGGCACCAAAAACGAGCACGAACGTCTCAAG                         ATTGAAGGGTATCCTACCATTCTCTTCTTCCCAGCAGGAGACAAGAGCGTT
genomic: TCGTGATTGCAAAGATGGATGGCACCAAAAACGAGCACGAACGTCTCAAGgttaatattc ... ccattcgcagATTGAAGGGTATCCTACCATTCTCTTCTTCCCAGCAGGAGACAAGAGCGTT
EST: gi|15261295|gb|BI436605.1|BI436605
EST:     TCGTGATTGCAAAGATGGATGGCACCAAAAACGAGCACGAACGTCTCAAG                         ATTGAAGGGTATCCTACCATTCTCTTCTTCCCAGCAGGAGACAAGAGCGTT
genomic: TCGTGATTGCAAAGATGGATGGCACCAAAAACGAGCACGAACGTCTCAAGgttaatattc ... ccattcgcagATTGAAGGGTATCCTACCATTCTCTTCTTCCCAGCAGGAGACAAGAGCGTT
EST: gi|37827776|gb|BJ585788.1|BJ585788
EST:     TCGTGATTGCAAAGATGGATGGCACCAAAAACGAGCACGAACGTCTCAAG                         ATTGAAGGGTATCCTACCATTCTCTTCTTCCCAGCAGGAGACAAGAGCGTT
genomic: TCGTGATTGCAAAGATGGATGGCACCAAAAACGAGCACGAACGTCTCAAGgttaatattc ... ccattcgcagATTGAAGGGTATCCTACCATTCTCTTCTTCCCAGCAGGAGACAAGAGCGTT
EST: gi|37840773|gb|BJ598781.1|BJ598781
EST:     TCGTGATTGCAAAGATGGATGGCACCAAAAACGAGCACGAACGTCTCAAG                         ATTGAAGGGTATCCTACCATTCTCTTCTTCCCAGCAGGAGACAAGAGCGTT
genomic: TCGTGATTGCAAAGATGGATGGCACCAAAAACGAGCACGAACGTCTCAAGgttaatattc ... ccattcgcagATTGAAGGGTATCCTACCATTCTCTTCTTCCCAGCAGGAGACAAGAGCGTT
EST: gi|18335249|gb|BJ167267.1|BJ167267
EST:     TCGTGATTGCAAAGATGGATGGCACCAAAAACGAGCACGAACGTCTCAAG                         ATTGAAGGGTATCTTACCATTCTCTTCTTCCCAGCAGGAGACAAGAGCGTC
genomic: TCGTGATTGCAAAGATGGATGGCACCAAAAACGAGCACGAACGTCTCAAGgttaatattc ... ccattcgcagATTGAAGGGTATCCTACCATTCTCTTCTTCCCAGCAGGAGACAAGAGCGTT
EST: gi|162181355|gb|FC357085.1|FC357085
EST:     TCGTGATTGCAAAGATGGATGGCACCAAAAACGAGCACGAACGTCTCAAG                         ATTGAAGGGTATCCTACCATTCTCTTCTTCCCAGCAGGAGACAAGAGCGTT
genomic: TCGTGATTGCAAAGATGGATGGCACCAAAAACGAGCACGAACGTCTCAAGgttaatattc ... ccattcgcagATTGAAGGGTATCCTACCATTCTCTTCTTCCCAGCAGGAGACAAGAGCGTT
EST: gi|37845794|gb|BJ603802.1|BJ603802
EST:     TCGTGATTGCAAAGATGGATGGCACCAAAAACGAGCACGAACGTCTCAAG                         ATTGAAGGGTATCCTACCATTCTCTTCTTCCCAGCAGGAGACAAGAGCGTT
genomic: TCGTGATTGCAAAGATGGATGGCACCAAAAACGAGCACGAACGTCTCAAGgttaatattc ... ccattcgcagATTGAAGGGTATCCTACCATTCTCTTCTTCCCAGCAGGAGACAAGAGCGTT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gctttaaaatcgttcgtgctctcttaacacgttctgtctggtgtaccattcgcagATTGAAGGGTATCCTACCATTCTCTTCTTCCCAGCAGGAGACAAGAGCGTTGAGCCT
                     tcttaac  putative branch site (score: 2)
     aaaat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gttaatattcctacttacgggtttcttgcttagcaattgaaacccaccccgatcttctcctaaattgcaaattgctttaaaatcgttcgtgctctcttaacacgttctgtctggtgtaccattcgcagATTGAAGGGTATCCTACCATTCTCTTCTTCCCAGCAGGAGACAAGAGCGTTGAGCCT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGGAGA