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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TACTGCAGACTCTCACTAAGGAGGATCTCAGCAAGATGTACTTCAGTGACTTCAAGGTCATTGACATCAATGGCTCCGAGTGTTTCCTCACCCGCACAGGgtatgtcgtcaccccctccaaaattttgcagagttcgctgcacttgtgctacctaatcatattctagacaaacctattttgtttttttgttaggttgcat...

Basic information

species Physcomitrella patens
transcript PP1S13_438V6.2
intron # 2
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S13_438V6.2 (Physcomitrella patens), 5'ss of exon 2
lower sequence: LOC_Os04g53230.1 (Oryza sativa), 5'ss of exon 2
TACTGCAGACTCTCACTAAGGAGGATCTCAGCAAGATGTACTTCAGTGACTTCAAGGTCATTGACATCAATGGCTCCGAGTGTTTCCTCACCCGCACAGGgtatg--tcgtc--accccct--ccaaaattttgcagagttcgctgc-acttgtgctacctaatcatattctagacaaacctattttgtttttttgttaggttgcat---
  || |||   || || || || ||| | ||||| ||||| ||||||||||||||| | |||||||||||||| |  |  || || |||||| | || |||||||  || |   | ||  |  ||||  | ||    |    ||| | || | || |   |     |||| |  |||   |||| |   | || ||  |  ||       
CTCTCCAGTTGCTGACAAAAGAAGATTTAAGCAAAATGTATTTCAGTGACTTCAAGATGATTGACATCAATGGATATGCTTGCTTTCTCACCAGAACTGGgtatgcttcatttgatcctttagccaagttgttaacaaccatgctactacctttgttttgtggaattattttgaaca---ctatgtcaatattctgagaatttcttacag

upper sequence: PP1S13_438V6.2 (Physcomitrella patens), 5'ss of exon 2
lower sequence: GRMZM5G876898_T01 (Zea mays), 5'ss of exon 2
TACTGCAGACTCTCACTAAGGAGGATCTCAGCAAGATGTACTTCAGTGACTTCAAGGTCATTGACATCAATGGCTCCGAGTGTTTCCTCACCCGCACAGGgtatgtcgtcaccccctc--caaaattttgcagagttcgctgcacttgtgctacctaatcatattctagacaaacctattttgtttttttgttaggttgcat
  ||||||   || || || || ||| | ||||| ||||||||||||||||||||| | |||||||||||||| |  |  || || || ||  | || ||||||  | ||    | |   |   ||| |           || |    |  |      || ||||  ||                                 
CTCTGCAGTTGCTGACGAAAGAAGATTTGAGCAAAATGTACTTCAGTGACTTCAAGATGATTGACATCAATGGATATGCATGCTTTCTGACGAGAACTGGgtatcacttcgattctttatcgccattatttgagcagtattgtaaggattgtcttatttcttatttcag---------------------------------
















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|100385965|gb|BY951159.1|BY951159
EST:     TTCAAGGTCATTGACATCAATGGCTCCGAGTGTTTCCTCACCCGCACAGG                         GTATACTGGCGAGGACGGTTTTGAGATTTCAGTGCCCGATGAATCTGCGCT
genomic: TTCAAGGTCATTGACATCAATGGCTCCGAGTGTTTCCTCACCCGCACAGGgtatgtcgtc ... gcggatgtagGTATACTGGCGAGGACGGTTTTGAGATTTCAGTGCCAGATGAATCTGCGCT
EST: gi|162168982|gb|FC345664.1|FC345664
EST:     TTCAAGGTCATTGACATCAATGGCTCCGAGTGTTTCCTCACCCGCACAGG                         GTATACTGGCGAGGACGGTTTTGAGATTTCAGTGCCAGATGAATCTGCGCT
genomic: TTCAAGGTCATTGACATCAATGGCTCCGAGTGTTTCCTCACCCGCACAGGgtatgtcgtc ... gcggatgtagGTATACTGGCGAGGACGGTTTTGAGATTTCAGTGCCAGATGAATCTGCGCT
EST: gi|37839941|gb|BJ597949.1|BJ597949
EST:     TCAAGGGTCATTGGCATCAATGGCTCCGAGTGTTTCCTCACCCGCACAGG                         GTATACTGGCGAGGACGGTTTTGAGATTTCAGTGCCAGATGAATCTGCGCT
genomic: TCAA-GGTCATTGACATCAATGGCTCCGAGTGTTTCCTCACCCGCACAGGgtatgtcgtc ... gcggatgtagGTATACTGGCGAGGACGGTTTTGAGATTTCAGTGCCAGATGAATCTGCGCT
EST: gi|100387175|gb|BY951574.1|BY951574
EST:     TTCAAGGTCATTGACATCAATGGCTCCGAGTGTTTCCTCACCCGCACAGG                         GTATACTGGCGAGGACGGTTTTGAGATTTCAGTGCCAGATGAATCTGCGCT
genomic: TTCAAGGTCATTGACATCAATGGCTCCGAGTGTTTCCTCACCCGCACAGGgtatgtcgtc ... gcggatgtagGTATACTGGCGAGGACGGTTTTGAGATTTCAGTGCCAGATGAATCTGCGCT
EST: gi|162181150|gb|FC357296.1|FC357296
EST:     TTCAAGGTCATTGACATCAATGGCTCCGAGTGTTTCCTCACCCGCACAGG                         GTATACTGGCGAGGACGGTTTTGAGATTTCAGTGCCAGATGAATCT
genomic: TTCAAGGTCATTGACATCAATGGCTCCGAGTGTTTCCTCACCCGCACAGGgtatgtcgtc ... gcggatgtagGTATACTGGCGAGGACGGTTTTGAGATTTCAGTGCCAGATGAATCT
EST: gi|37824945|gb|BJ583011.1|BJ583011
EST:     TTCAAGGTCATTGACATCAATGGCTCCGAGTGTTTCCTCACCCGCACAGG                         GTATACTGGCGAGGACGGTTTTGAGATTTCAGTGCCAGATGAATCTGCGCT
genomic: TTCAAGGTCATTGACATCAATGGCTCCGAGTGTTTCCTCACCCGCACAGGgtatgtcgtc ... gcggatgtagGTATACTGGCGAGGACGGTTTTGAGATTTCAGTGCCAGATGAATCTGCGCT
EST: gi|162180577|gb|FC356934.1|FC356934
EST:     GGTCATTGACATCAATGGCTCCGAGTGTTTCCTCACCCGCACAGG                         GTATACTGGCGAGGACGGTTNTGAGATTTCAGTGCCAGATGAATCTGCGCT
genomic: GGTCATTGACATCAATGGCTCCGAGTGTTTCCTCACCCGCACAGGgtatgtcgtc ... gcggatgtagGTATACTGGCGAGGACGGTTTTGAGATTTCAGTGCCAGATGAATCTGCGCT
EST: gi|162255662|gb|FC431660.1|FC431660
EST:     TTCAAGGTCATTGACATCAATGGCTCCGAGTGTTTCCTCACCCGCACAGG                         GTATACTGGCGAGGACGGTTTTGAGATTTCAGTGCCAGATGAATCTGCGCT
genomic: TTCAAGGTCATTGACATCAATGGCTCCGAGTGTTTCCTCACCCGCACAGGgtatgtcgtc ... gcggatgtagGTATACTGGCGAGGACGGTTTTGAGATTTCAGTGCCAGATGAATCTGCGCT
EST: gi|19779833|gb|BQ039481.1|BQ039481
EST:     TTCAAGGTCATTGACATCAATGGCTCCGAGTGTTTCCTCACCCGCACAGG                         GTATACTGGCGAGGACGGTTTTGAGATTTCAGTGCCAGATGAATCTGCGCT
genomic: TTCAAGGTCATTGACATCAATGGCTCCGAGTGTTTCCTCACCCGCACAGGgtatgtcgtc ... gcggatgtagGTATACTGGCGAGGACGGTTTTGAGATTTCAGTGCCAGATGAATCTGCGCT
EST: gi|162218905|gb|FC395150.1|FC395150
EST:     TTCAAGGTCATTGACATCAATGGCTCCGAGTGTTTCCTCACCCGCACAGG                         GTATACTGGCGAGGACGGTTTTGAGATTTCAGTGCCAGATGAATCTGCGCT
genomic: TTCAAGGTCATTGACATCAATGGCTCCGAGTGTTTCCTCACCCGCACAGGgtatgtcgtc ... gcggatgtagGTATACTGGCGAGGACGGTTTTGAGATTTCAGTGCCAGATGAATCTGCGCT
EST: gi|162216811|gb|FC392187.1|FC392187
EST:     TTCAAGGTCATTGACATCAATGGCTCCGAGTGTTTCCTCACCCGCACAGG                         GTATACTGGCGAGGACGGTTTTGAGATTTCAGTGCCAGATGAATCTGCGCT
genomic: TTCAAGGTCATTGACATCAATGGCTCCGAGTGTTTCCTCACCCGCACAGGgtatgtcgtc ... gcggatgtagGTATACTGGCGAGGACGGTTTTGAGATTTCAGTGCCAGATGAATCTGCGCT
EST: gi|162247043|gb|FC422217.1|FC422217
EST:     TTCAAGGTCATTGACATCAATGGCTCCGAGTGTTTCCTCACCCGCACAGG                         GTATACTGGCGAGGACGGTTTTGAGATTTCAGTGCCAGATGAATCTGCGCT
genomic: TTCAAGGTCATTGACATCAATGGCTCCGAGTGTTTCCTCACCCGCACAGGgtatgtcgtc ... gcggatgtagGTATACTGGCGAGGACGGTTTTGAGATTTCAGTGCCAGATGAATCTGCGCT
EST: gi|162236584|gb|FC413159.1|FC413159
EST:     TTCAAGGTCATTGACATCAATGGCTCCGAGTGTTTCCTCACCCGCACAGG                         GTATACTGGCGAGGACGGTTTTGAGATTTCAGTGGCAGATGAATCTGCGCT
genomic: TTCAAGGTCATTGACATCAATGGCTCCGAGTGTTTCCTCACCCGCACAGGgtatgtcgtc ... gcggatgtagGTATACTGGCGAGGACGGTTTTGAGATTTCAGTGCCAGATGAATCTGCGCT
EST: gi|162167827|gb|FC344557.1|FC344557
EST:     TTCAAGGTCATTGACATCAATGGCTCCGAGTGTTTCCTCACCCGCACAGG                         GTATACTGGCGAGGACGGTTTTGAGATTTCAGTGCCAGATGAATCTGCGCT
genomic: TTCAAGGTCATTGACATCAATGGCTCCGAGTGTTTCCTCACCCGCACAGGgtatgtcgtc ... gcggatgtagGTATACTGGCGAGGACGGTTTTGAGATTTCAGTGCCAGATGAATCTGCGCT
EST: gi|37852132|gb|BJ610140.1|BJ610140
EST:     TTCAAGGTCATTGGCATCAATGGCTCCGAGTGTTTCCTCACCCGCACAGG                         GTATACTGGCGAGGACGGTTTTGAGATTTCAGTGCCAGATGAATCTGCGCT
genomic: TTCAAGGTCATTGACATCAATGGCTCCGAGTGTTTCCTCACCCGCACAGGgtatgtcgtc ... gcggatgtagGTATACTGGCGAGGACGGTTTTGAGATTTCAGTGCCAGATGAATCTGCGCT
EST: gi|100380347|gb|BY986667.1|BY986667
EST:     TTCAAGGTCATTGACATCAATGGCTCCGAGTGTTTCCTCACCCGCACAGG                         GTATACTGGCGAGGACGGTTTTGAGATTTCAGTGCCAGATGAATCTGCGCT
genomic: TTCAAGGTCATTGACATCAATGGCTCCGAGTGTTTCCTCACCCGCACAGGgtatgtcgtc ... gcggatgtagGTATACTGGCGAGGACGGTTTTGAGATTTCAGTGCCAGATGAATCTGCGCT
EST: gi|162168981|gb|FC345663.1|FC345663
EST:     CGAGTGTTTCCTCACCCGCACAGG                         GTATACTGGCGAGGACGGTTTTGAGATTTCAGTGCCAGATGAATCTGCGCT
genomic: CGAGTGTTTCCTCACCCGCACAGGgtatgtcgtc ... gcggatgtagGTATACTGGCGAGGACGGTTTTGAGATTTCAGTGCCAGATGAATCTGCGCT
EST: gi|162276148|gb|FC452840.1|FC452840
EST:     CACCCGCACAGG                         GTATACTGGCGAGGACGGTTTTGAGATTTCAGTGCCAGATGAATCTGCGCT
genomic: CACCCGCACAGGgtatgtcgtc ... gcggatgtagGTATACTGGCGAGGACGGTTTTGAGATTTCAGTGCCAGATGAATCTGCGCT
EST: gi|100452928|gb|CJ975514.1|CJ975514
EST:     TTCAAGGTCATTGACATCAATGGCTCCAAGTGTTTCCTCACCCGCACAGG                         GTATACTGGCGAGGACG
genomic: TTCAAGGTCATTGACATCAATGGCTCCGAGTGTTTCCTCACCCGCACAGGgtatgtcgtc ... gcggatgtagGTATACTGGCGAGGACG
EST: gi|162175937|gb|FC351615.1|FC351615
EST:     TTCAAGGTCATTGACATCAATGGCTCCGAGTGTTTCCTCACCCGCACAGG                         GTATACTGGCGAGGACGGTTTTGAGATTTCAGTGCCAGATGAATCTGCGCT
genomic: TTCAAGGTCATTGACATCAATGGCTCCGAGTGTTTCCTCACCCGCACAGGgtatgtcgtc ... gcggatgtagGTATACTGGCGAGGACGGTTTTGAGATTTCAGTGCCAGATGAATCTGCGCT
EST: gi|162189394|gb|FC366552.1|FC366552
EST:     TTCAAGGTCATTGACATCAATGGCTCCGAGTGTTTCCTCACCCGCACAGG                         GTATACTGGCGAGGACGGTTTTGAGATTTCAGTGCCAGATGAATCTGCGCT
genomic: TTCAAGGTCATTGACATCAATGGCTCCGAGTGTTTCCTCACCCGCACAGGgtatgtcgtc ... gcggatgtagGTATACTGGCGAGGACGGTTTTGAGATTTCAGTGCCAGATGAATCTGCGCT

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: 35 (upstream exon), 35 (downstream exon)
Score: 23

TACTGCAGACTCTCACTAAGGAGGATCTCAGCAAGATGTACTTCAGTGACTTCAAGGTCATTGACATCAATGGCTCCGAGTGTTTCCTCACCCGCACAGGgtatgtcgtc ... gcggatgtagGTATACTGGCGAGGACGGTTTTGAGATTTCAGTGCCAGATGAATCTGCGCTCGATTTGACAAAGGCAATCATGGACAAGGGTCAGGGAAAGATTCGCCTA




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