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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtactttatcactgaaaataaattgaagttctttttttcatccttttatgtactaatggcgttcttcgtttctacagCTCCAGAACATAAAATCTGAAATAGCTGATGCGTCTGCTAATCCTCAAGGTCTACTTCTGGAGGCCCTTCATTCGGTTGGATATTCCGGGGCACTGGCAA

Basic information

species Zea mays
transcript GRMZM2G005036_T01
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G005036_T01 (Zea mays), 3'ss of exon 3
lower sequence: LOC_Os05g44916.1 (Oryza sativa), 3'ss of exon 3
gtactttatcact--gaaaataaattgaagttctttttttcatccttttatgtactaatggc-gttcttcgtttctacagCTCCAGAACATAAAATCTGAAATAGCTGATGCGTCTGCTAATCCTCAAGGTCTACTTCTGGAGGCCCTTCATTCGGTTGGATATTCCGGGGCACTGGCAA
|| | | |||| |  ||  || |  |   | |  ||||       |||||   | || |    | |  | | |||||||||||||||| ||||||||||||||| |||| | ||||| | |||| || ||||||||| |||| || || ||||||| ||||||||| ||||| |||||||
gtgcatgatcattttgagcattatatttcgctaattttgcttcttttttactgattattatttgctaattgcttctacagCTCCAGAAGATAAAATCTGAAATATCTGAAGTGTCTGGTGATCCACATGGTCTACTTATGGAAGCGCTCCATTCGGCTGGATATTCTGGGGCTCTGGCAA
















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|149042117|gb|EE047095.2|EE047095
EST:     TTGACAGTGTGAGGAATCCAGCATTCCTCGATTGGGAGGTCAAAGAGCAG                         CTCCAGAACATAAAATCTGAAATAGCTGATGCGTCTGCTAATCCTCAAGGT
genomic: TTGACAGTGTGAGGAATCCAGCATTCCTCGATTGGGAGGTCAAAGAGCAGgtactttatc ... gtttctacagCTCCAGAACATAAAATCTGAAATAGCTGATGCGTCTGCTAATCCTCAAGGT
EST: gi|71764445|gb|DR962382.1|DR962382
EST:     TTGACAGTGTGAGGAATCCAGCATTCCTCGATTGGGAGGTCAAAGAGCAG                         CTCCAGAACATAAAATCTGAAATAGCTGATGCGTCTGCTAATCCTCAAGGT
genomic: TTGACAGTGTGAGGAATCCAGCATTCCTCGATTGGGAGGTCAAAGAGCAGgtactttatc ... gtttctacagCTCCAGAACATAAAATCTGAAATAGCTGATGCGTCTGCTAATCCTCAAGGT
EST: gi|31356317|gb|CD440674.1|CD440674
EST:     TTGACAGTGTGAGGAATCCAGCATTCCTCGATTGGGAGGTCAAAGAGCAG                         CTCCAGAACATAAAATCTGAAATAGCTGATGCGTCTGCTAATCCTCAAGGT
genomic: TTGACAGTGTGAGGAATCCAGCATTCCTCGATTGGGAGGTCAAAGAGCAGgtactttatc ... gtttctacagCTCCAGAACATAAAATCTGAAATAGCTGATGCGTCTGCTAATCCTCAAGGT
EST: gi|88755467|gb|DY539608.1|DY539608
EST:     TTGACAGTGTGAGGAATCCAGCATTCCTCGATTGGGAGGTCAAAGAGCAG                         CTCCAGAACATAAAATCTGAAATAGCTGATGCGTCTGCTAATCCTCAAG
genomic: TTGACAGTGTGAGGAATCCAGCATTCCTCGATTGGGAGGTCAAAGAGCAGgtactttatc ... gtttctacagCTCCAGAACATAAAATCTGAAATAGCTGATGCGTCTGCTAATCCTCAAG
EST: gi|89761459|gb|DY689465.1|DY689465
EST:     TTGACAGTGTGAGGAATCCAGCATTCCTCGATTGGGAGGTCAAAGAGCAG                         CTCCAGAACATAAAATCTGAAATAGCTGATGCGTCTGCTAATCCTCAAGGT
genomic: TTGACAGTGTGAGGAATCCAGCATTCCTCGATTGGGAGGTCAAAGAGCAGgtactttatc ... gtttctacagCTCCAGAACATAAAATCTGAAATAGCTGATGCGTCTGCTAATCCTCAAGGT
EST: gi|76935641|gb|DV174409.1|DV174409
EST:     TTGACAGTGTGAGGAATCCAGCATTCCTCGATTGGGAGGTCAAAGAGCAG                         CTCCAGAACATAAAATCTGAAATAGCTGATGCGTCTGCTAATCCTCAAGGT
genomic: TTGACAGTGTGAGGAATCCAGCATTCCTCGATTGGGAGGTCAAAGAGCAGgtactttatc ... gtttctacagCTCCAGAACATAAAATCTGAAATAGCTGATGCGTCTGCTAATCCTCAAGGT
EST: gi|211340942|gb|FL378185.1|FL378185
EST:     TTGACAGTGTGAGGAATCCAGCATTCCTCGATTGGGAGGTCAAAGAGCAG                         CTCCAGAACATAAAA
genomic: TTGACAGTGTGAGGAATCCAGCATTCCTCGATTGGGAGGTCAAAGAGCAGgtactttatc ... gtttctacagCTCCAGAACATAAAA
EST: gi|211273249|gb|FL384317.1|FL384317
EST:     TTGACAGTGTGAGGAATCCAGCATTCCTCGATTGGGAGGTCAAAGAGCAG                         CTCCAGAACATAAAATCTGAAATAGCTGATGCGTCTGCTAATCCTCAAGGT
genomic: TTGACAGTGTGAGGAATCCAGCATTCCTCGATTGGGAGGTCAAAGAGCAGgtactttatc ... gtttctacagCTCCAGAACATAAAATCTGAAATAGCTGATGCGTCTGCTAATCCTCAAGGT
EST: gi|31358559|gb|CD442916.1|CD442916
EST:     TTGACAGTGTGAGGAATCCAGCATTCCTCGATTGGGAGGTCAAAGAGCAG                         CTCCAGAACATAAAATCTGAAATAGCTGATGCGTCTGCTAATCCTCAAGGT
genomic: TTGACAGTGTGAGGAATCCAGCATTCCTCGATTGGGAGGTCAAAGAGCAGgtactttatc ... gtttctacagCTCCAGAACATAAAATCTGAAATAGCTGATGCGTCTGCTAATCCTCAAGGT
EST: gi|31354401|gb|CD438758.1|CD438758
EST:     TTGACAGTGTGAGGAATCCAGCATTCCTCGATTGGGAGGTCAAAGAGCAG                         CTCCAGAACATAAAATCTGAAATAGCTGATGCGTCTGCTAATCCTCAAGGT
genomic: TTGACAGTGTGAGGAATCCAGCATTCCTCGATTGGGAGGTCAAAGAGCAGgtactttatc ... gtttctacagCTCCAGAACATAAAATCTGAAATAGCTGATGCGTCTGCTAATCCTCAAGGT
EST: gi|31353102|gb|CD437459.1|CD437459
EST:     TTGACAGTGTGAGGAATCCAGCATTCCTCGATTGGGAGGTCAAAGAGCAG                         CTCCAGAACATAAAATCTGAAATAGCTGATGCGTCTGCTAATCCTCAAGGT
genomic: TTGACAGTGTGAGGAATCCAGCATTCCTCGATTGGGAGGTCAAAGAGCAGgtactttatc ... gtttctacagCTCCAGAACATAAAATCTGAAATAGCTGATGCGTCTGCTAATCCTCAAGGT
EST: gi|211411533|gb|FL428561.1|FL428561
EST:     TGACAGTGTGAGGAATCCAGCATTCCTCGATTGGGAGGTNCAA-GAGCAG                         CTCCAGAACATAAAATCTGAAATAGCTGATGCGTCTGCTAATCCTCAAGGT
genomic: TGACAGTGTGAGGAATCCAGCATTCCTCGATTGGGAGGT-CAAAGAGCAGgtactttatc ... gtttctacagCTCCAGAACATAAAATCTGAAATAGCTGATGCGTCTGCTAATCCTCAAGGT
EST: gi|19770121|gb|BQ034842.1|BQ034842
EST:     TTGACAGTGTGAGGAATCCAGCATTCCTCGATTGGGAGGTCAAAGAGCAG                         CTCCAGAACATAAAATCTGAAATAGCTGATGCGTCTGCTAATCCTCAAGGT
genomic: TTGACAGTGTGAGGAATCCAGCATTCCTCGATTGGGAGGTCAAAGAGCAGgtactttatc ... gtttctacagCTCCAGAACATAAAATCTGAAATAGCTGATGCGTCTGCTAATCCTCAAGGT
EST: gi|76912595|gb|DV164810.1|DV164810
EST:     TTGACAGTGTGAGGAATCCAGCATTCCTCGATTGGGAGGTCAAAGAGCAG                         CTCCAGAACATAAAATCTGAAATAGCTGATGCGTCTGCTAATCCTCAAGGT
genomic: TTGACAGTGTGAGGAATCCAGCATTCCTCGATTGGGAGGTCAAAGAGCAGgtactttatc ... gtttctacagCTCCAGAACATAAAATCTGAAATAGCTGATGCGTCTGCTAATCCTCAAGGT
EST: gi|78092878|gb|DV521252.1|DV521252
EST:     TTGACAGTGTGAGGAATCCAGCATTCCTCGATTGGGAGGTCAAAGAGCAG                         CTCCAGAACATAAAATCTGAAATAGCTGATGCGTCTGCTAATCCTCAAGGT
genomic: TTGACAGTGTGAGGAATCCAGCATTCCTCGATTGGGAGGTCAAAGAGCAGgtactttatc ... gtttctacagCTCCAGAACATAAAATCTGAAATAGCTGATGCGTCTGCTAATCCTCAAGGT
EST: gi|31354663|gb|CD439020.1|CD439020
EST:     TTGACAGTGTGAGGAATCCAGCATTCCTCGATTGGGAGGTCAAAGAGCAG                         CTCCAGAACATAAAATCTGAAATAGCTGATGCGTCTGCTAATCCTCAAGGT
genomic: TTGACAGTGTGAGGAATCCAGCATTCCTCGATTGGGAGGTCAAAGAGCAGgtactttatc ... gtttctacagCTCCAGAACATAAAATCTGAAATAGCTGATGCGTCTGCTAATCCTCAAGGT
EST: gi|148965824|gb|EE016713.2|EE016713
EST:     TTGACAGTGTGAGGAATCCAGCATTCCTCGATTGGGAGGTCAAAGAGCAG                         CTCCAGAACATAAAATCTGAAATAGCTGATGCGTCTGCTAATCCTCAAGGT
genomic: TTGACAGTGTGAGGAATCCAGCATTCCTCGATTGGGAGGTCAAAGAGCAGgtactttatc ... gtttctacagCTCCAGAACATAAAATCTGAAATAGCTGATGCGTCTGCTAATCCTCAAGGT
EST: gi|148944905|gb|EC890064.2|EC890064
EST:     TTGACAGTGTGAGGAATCCAGCATTCCTCGATTGGGAGGTCAAAGAGCAG                         CTCCAGAACATAAAATCTGAAATAGCTGATGCGTCTGCTAATCCTCAAGGT
genomic: TTGACAGTGTGAGGAATCCAGCATTCCTCGATTGGGAGGTCAAAGAGCAGgtactttatc ... gtttctacagCTCCAGAACATAAAATCTGAAATAGCTGATGCGTCTGCTAATCCTCAAGGT
EST: gi|32837193|gb|CD976871.1|CD976871
EST:     TTGACAGTGTGAGGAATCCAGCATTCCTCGATTGGGAGGTCAAAGAGCAG                         CTCCAGAACATAAAATCTGAAATAGCTGATGTGTCTGCTAATCCTCAAGGT
genomic: TTGACAGTGTGAGGAATCCAGCATTCCTCGATTGGGAGGTCAAAGAGCAGgtactttatc ... gtttctacagCTCCAGAACATAAAATCTGAAATAGCTGATGCGTCTGCTAATCCTCAAGGT
EST: gi|89247626|gb|DY619412.1|DY619412
EST:     TTGACAGTGTGAGGAATCCAGCATTCCTCGATTGGGAGGTCAAAGAGCAG                         CTCCAGAACATAAAATCTGAAATAGCTGATGCGTCTGCTAATCCTCAAGGT
genomic: TTGACAGTGTGAGGAATCCAGCATTCCTCGATTGGGAGGTCAAAGAGCAGgtactttatc ... gtttctacagCTCCAGAACATAAAATCTGAAATAGCTGATGCGTCTGCTAATCCTCAAGGT
EST: gi|211381649|gb|FL369275.1|FL369275
EST:     TTGACAGTGTGAAGAATCCAGCATTCCTCGATTGGGAGGTCAAAGAGCAG                         CTCCAGAACATAAAATCTGAAATAGCTGATGCGTCTGCTAATCCTCAAGGT
genomic: TTGACAGTGTGAGGAATCCAGCATTCCTCGATTGGGAGGTCAAAGAGCAGgtactttatc ... gtttctacagCTCCAGAACATAAAATCTGAAATAGCTGATGCGTCTGCTAATCCTCAAGGT
EST: gi|78106581|gb|DV524999.1|DV524999
EST:     TTGACAGTGTGAGGAATCCAGCATTCCTCGATTGGGAGGTCAAAGAGCAG                         CTCCAGAACATAAAATCTGAAATAGCTGATGCGTCTGCTAATCCTCAAGGT
genomic: TTGACAGTGTGAGGAATCCAGCATTCCTCGATTGGGAGGTCAAAGAGCAGgtactttatc ... gtttctacagCTCCAGAACATAAAATCTGAAATAGCTGATGCGTCTGCTAATCCTCAAGGT
EST: gi|19822381|gb|BQ048405.1|BQ048405
EST:     TTGACAGTGTGAGGAATCCAGCATTCCTCGATTGGGAGGTCAAAGAGCAG                         CTCCAGAACATAAAATCTGAAATAGCTGATGCGTCTGCTAATCCTCAAGGT
genomic: TTGACAGTGTGAGGAATCCAGCATTCCTCGATTGGGAGGTCAAAGAGCAGgtactttatc ... gtttctacagCTCCAGAACATAAAATCTGAAATAGCTGATGCGTCTGCTAATCCTCAAGGT
EST: gi|149081535|gb|EE170671.2|EE170671
EST:     TTGACAGTGTGAGGAATCCAGCATTCCTCGATTGGGAGGTCAAAGAGCAG                         CTCCAGAACATAAAATCTGAAATAGCTGATGCGTCTGCTAATCCTCAAGGT
genomic: TTGACAGTGTGAGGAATCCAGCATTCCTCGATTGGGAGGTCAAAGAGCAGgtactttatc ... gtttctacagCTCCAGAACATAAAATCTGAAATAGCTGATGCGTCTGCTAATCCTCAAGGT
EST: gi|31349354|gb|CD433711.1|CD433711
EST:     TTGACAGTGTGAGGAATCCAGCATTCCTCGATTGGGAGGTCAAAGAGCAG                         CTCCAGAACATAAAATCTGAAATAGCTGATGCGTCTGCTAATCCTCAAGGT
genomic: TTGACAGTGTGAGGAATCCAGCATTCCTCGATTGGGAGGTCAAAGAGCAGgtactttatc ... gtttctacagCTCCAGAACATAAAATCTGAAATAGCTGATGCGTCTGCTAATCCTCAAGGT
EST: gi|211159959|gb|FL410900.1|FL410900
EST:     TGACAGTGTGAGGAATCCAGCATTCCTCGATTGGGAGGGTCAA-GAGCAG                         CTCCAGAACATAAAATCTGAAATAGCTGATGCGTCTGCTAATCCTCAAG-T
genomic: TGACAGTGTGAGGAATCCAGCATTCCTCGATTGGGAGG-TCAAAGAGCAGgtactttatc ... gtttctacagCTCCAGAACATAAAATCTGAAATAGCTGATGCGTCTGCTAATCCTCAAGGT
EST: gi|30031572|gb|CB833423.1|CB833423
EST:     TTGACAG-GTGAGGAATCCAGCATTCCTCGATTGGGAGGTCAAAGAGCAG                         CTCCAGAACATAAAATCTGAAATAGCTGATGCGTCTGCTAATCCTCAAGGT
genomic: TTGACAGTGTGAGGAATCCAGCATTCCTCGATTGGGAGGTCAAAGAGCAGgtactttatc ... gtttctacagCTCCAGAACATAAAATCTGAAATAGCTGATGCGTCTGCTAATCCTCAAGGT

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 4 RNA-Seq libraries.


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 312

TACCTATGATGCATTGAAGAGCTATACACCAGAAATGGTTGAAGTTCTCATTGACAGTGTGAGGAATCCAGCATTCCTCGATTGGGAGGTCAAAGAGCAGgtactttatc ... gtttctacagCTCCAGAACATAAAATCTGAAATAGCTGATGCGTCTGCTAATCCTCAAGGTCTACTTCTGGAGGCCCTTCATTCGGTTGGATATTCCGGGGCACTGGCAA


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 172

TACCTATGATGCATTGAAGAGCTATACACCAGAAATGGTTGAAGTTCTCATTGACAGTGTGAGGAATCCAGCATTCCTCGATTGGGAGGTCAAAGAGCAGgtactttatc ... gtttctacagCTCCAGAACATAAAATCTGAAATAGCTGATGCGTCTGCTAATCCTCAAGGTCTACTTCTGGAGGCCCTTCATTCGGTTGGATATTCCGGGGCACTGGCAA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 251

TACCTATGATGCATTGAAGAGCTATACACCAGAAATGGTTGAAGTTCTCATTGACAGTGTGAGGAATCCAGCATTCCTCGATTGGGAGGTCAAAGAGCAGgtactttatc ... gtttctacagCTCCAGAACATAAAATCTGAAATAGCTGATGCGTCTGCTAATCCTCAAGGTCTACTTCTGGAGGCCCTTCATTCGGTTGGATATTCCGGGGCACTGGCAA


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 362

TACCTATGATGCATTGAAGAGCTATACACCAGAAATGGTTGAAGTTCTCATTGACAGTGTGAGGAATCCAGCATTCCTCGATTGGGAGGTCAAAGAGCAGgtactttatc ... gtttctacagCTCCAGAACATAAAATCTGAAATAGCTGATGCGTCTGCTAATCCTCAAGGTCTACTTCTGGAGGCCCTTCATTCGGTTGGATATTCCGGGGCACTGGCAA




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttgaagttctttttttcatccttttatgtactaatggcgttcttcgtttctacagCTCCAGAACATAAAATCTGAAATAGCTGATGCGTCTGCTAATCCTCAAGGTCTACTTCTGGAGGCCCTTCATTCGGTTGGATATTCCGGGGCACTGGCAA
                            tactaat  putative branch site (score: 362)
                                     cgttcttcgtttct  putative PPT
                     ttttatgtactaat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtactttatcactgaaaataaattgaagttctttttttcatccttttatgtactaatggcgttcttcgtttctacagCTCCAGAACATAAAATCTGAAATAGCTGATGCGTCTGCTAATCCTCAAGGTCTACTTCTGGAGGCCCTTCATTCGGTTGGATATTCCGGGGCACTGGCAA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAGG