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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagtgttcactttctcctttactttatactatcaatatttcttcaacttatacaccatcagtaccaaaaaaaaaatcttatttattcaatccatagctgatacaaattttctaccctgttacctgaaaatagGTGAAACGTAATGGTGTGTCCATCTTCCTCATGCCATCTGGAACAATTGGCACACTTCGAGCACTCTGGGATGTCTTCCCTCTGTTCACAAATACTGCAT

Basic information

species Zea mays
transcript GRMZM2G139374_T01
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G139374_T02 (Zea mays), 3'ss of exon 2
lower sequence: LOC_Os01g58114.2 (Oryza sativa), 3'ss of exon 2
gtaagtgttcactttctcctttactttatactatcaatatttcttcaacttatacaccatcagtaccaaaaaaaaaatcttatttattcaatccatagctgatacaaattttc-taccctgttacctgaaaatagGTGAAACGTAATGGTGTGTCCATCTTCCTCATGCCATCTGGAACAATTGGCACACTTCGAGCACTCTGGGATGTCTTCCCTCTGTTCACAAATACTGCAT
                                                  ||    ||  | | | |          | | ||           ||   ||||||| || | | |   || |||||| || |||||| ||||| || || || ||||| ||||| |||||||||||||||||||| |||||| ||||||| |||||||| ||||| ||||| |||||||||  ||
-------------------------------------------------gtaagtccccgctgcagctgcttttgtttgtaatcagcatttctgatcattgatacacatatgcatgatcttttaccttaacatagGTAAAACGCAAAGGAGTATCCATATTCCTGATGCCATCTGGAACAATTGGAACACTTAGAGCACTTTGGGATGTTTTCCCCCTGTTTACAAATACTCAAT
















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|110202367|gb|EC884264.1|EC884264
EST:     AGCACACTCTTGATATCAAAGAATGGGAAAGCGAGGCTGAGTATGAGTAT                         GTGAAACGTAATGGTGTGTCCATCTTCCTCATGCCATCTGGAACAATTGGC
genomic: AGCACACTCTTGATATCAAAGAATGGGAAAGCGAGGCTGAGTATGAGTATgtaagtgttc ... ctgaaaatagGTGAAACGTAATGGTGTGTCCATCTTCCTCATGCCATCTGGAACAATTGGC
EST: gi|211004797|gb|FL233607.1|FL233607
EST:     AGCACACTCTTGATATCAAAGAATGGGAAAGCGATGCTGAGTATGAGTAT                         GTGAAACGTAATGGTGTGTCCCAT-TTCCTCATGCCATCTGGAACAATTGG
genomic: AGCACACTCTTGATATCAAAGAATGGGAAAGCGAGGCTGAGTATGAGTATgtaagtgttc ... ctgaaaatagGTGAAACGTAATGGTGTGTCC-ATCTTCCTCATGCCATCTGGAACAATTGG
EST: gi|148931314|gb|EC874175.2|EC874175
EST:     AGCACACTCTTGATATCAAAGAATGGGAAAGCGAGGCTGAGTATGAGTAT                         GTGAAACGTAATGGTGTGTCCATCTTCCTCATGCCATCTGGAACAATTGGC
genomic: AGCACACTCTTGATATCAAAGAATGGGAAAGCGAGGCTGAGTATGAGTATgtaagtgttc ... ctgaaaatagGTGAAACGTAATGGTGTGTCCATCTTCCTCATGCCATCTGGAACAATTGGC
EST: gi|93284093|gb|EB676357.1|EB676357
EST:     AGCACACTCTTGATATCAAAGAATGGGAAAGCGAGGCTGAGTATGAGTAT                         GTGAAACGTAATGGTGTGTCCATCTTCCTCATGCCATCTGGAACAATTGGC
genomic: AGCACACTCTTGATATCAAAGAATGGGAAAGCGAGGCTGAGTATGAGTATgtaagtgttc ... ctgaaaatagGTGAAACGTAATGGTGTGTCCATCTTCCTCATGCCATCTGGAACAATTGGC
EST: gi|148955706|gb|EC901392.2|EC901392
EST:     AGCACACTCTTGATATCAAAGAATGGGAAAGCGAGGCTGAGTATGAGTAT                         GTGAAACGTAATGGTGTGTCCATCTTCCTCATGCCATCTGGAACAATTGGC
genomic: AGCACACTCTTGATATCAAAGAATGGGAAAGCGAGGCTGAGTATGAGTATgtaagtgttc ... ctgaaaatagGTGAAACGTAATGGTGTGTCCATCTTCCTCATGCCATCTGGAACAATTGGC
EST: gi|76011882|gb|DT939052.1|DT939052
EST:     AGCACACTCTTGATATCAAAGAATGGGAAAGCGAGGCTGAGTATGAGTAT                         GTGAAACGTAATGGTGTGTCCATCTTCCTCATGCCATCTGGAACAATTGGC
genomic: AGCACACTCTTGATATCAAAGAATGGGAAAGCGAGGCTGAGTATGAGTATgtaagtgttc ... ctgaaaatagGTGAAACGTAATGGTGTGTCCATCTTCCTCATGCCATCTGGAACAATTGGC
EST: gi|149110172|gb|EE293987.2|EE293987
EST:     AGCACACTCTTGATATCAAAGAATGGGAAAGCGAGGCTGAGTATGAGTAT                         GTGAAACGTAATGGTGTGTCCATCTTCCTCATGCCATCTGGAACAATTGGC
genomic: AGCACACTCTTGATATCAAAGAATGGGAAAGCGAGGCTGAGTATGAGTATgtaagtgttc ... ctgaaaatagGTGAAACGTAATGGTGTGTCCATCTTCCTCATGCCATCTGGAACAATTGGC
EST: gi|74235211|gb|DT643125.1|DT643125
EST:     AGCACACTCTTGATATCAAAGAATGGGAAAGCGAGGCTGAGTATGAGTAT                         GTGAAACGTAATGGTGTGTCCATCTTCCTCATGCCATCTGGAACAATTGGC
genomic: AGCACACTCTTGATATCAAAGAATGGGAAAGCGAGGCTGAGTATGAGTATgtaagtgttc ... ctgaaaatagGTGAAACGTAATGGTGTGTCCATCTTCCTCATGCCATCTGGAACAATTGGC
EST: gi|32823063|gb|CD962772.1|CD962772
EST:     AGCACACTCTTGATATCAAAGAATGGGAAAGCGAGGCTGAGTATGAGTAT                         GTGAAACGTAATGGTGTGTCCATCTTCCTCATGCCATCTGGAACAATTGGC
genomic: AGCACACTCTTGATATCAAAGAATGGGAAAGCGAGGCTGAGTATGAGTATgtaagtgttc ... ctgaaaatagGTGAAACGTAATGGTGTGTCCATCTTCCTCATGCCATCTGGAACAATTGGC
EST: gi|148965948|gb|EE016864.2|EE016864
EST:     AGCACACTCTTGATATCAAAGAATGGGAAAGCGAGGCTGAGTATGAGTAT                         GTGAAACGTAATGGTGTGTCCATCTTCCTCATGCCATCTGGAACAATTGGC
genomic: AGCACACTCTTGATATCAAAGAATGGGAAAGCGAGGCTGAGTATGAGTATgtaagtgttc ... ctgaaaatagGTGAAACGTAATGGTGTGTCCATCTTCCTCATGCCATCTGGAACAATTGGC
EST: gi|149079827|gb|EE168827.2|EE168827
EST:     AGCACACTCTTGATATCAAAGAATGGGAAAGCGAGGCTGAGTATGAGTAT                         GTGAAACGTAATGGTGTGTCCATCTTCCTCATGCCATCTGGAACAATTGGC
genomic: AGCACACTCTTGATATCAAAGAATGGGAAAGCGAGGCTGAGTATGAGTATgtaagtgttc ... ctgaaaatagGTGAAACGTAATGGTGTGTCCATCTTCCTCATGCCATCTGGAACAATTGGC
EST: gi|148946744|gb|EC892010.2|EC892010
EST:     AGCACACTCTTGATATCAAAGAATGGGAAAGCGAGGCTGAGTATGAGTAT                         GTGAAACGTAATGGTGTGTCCATCTTCCTCATGCCATCTGGAACAATTGGC
genomic: AGCACACTCTTGATATCAAAGAATGGGAAAGCGAGGCTGAGTATGAGTATgtaagtgttc ... ctgaaaatagGTGAAACGTAATGGTGTGTCCATCTTCCTCATGCCATCTGGAACAATTGGC
EST: gi|148967020|gb|EE018178.2|EE018178
EST:     AGCACACTCTTGATATCAAAGAATGGGAAAGCGAGGCTGAGTATGAGTAT                         GTGAAACGTAATGGTGTGTCCATCTTCCTCATGCCATCTGGAACAATTGGC
genomic: AGCACACTCTTGATATCAAAGAATGGGAAAGCGAGGCTGAGTATGAGTATgtaagtgttc ... ctgaaaatagGTGAAACGTAATGGTGTGTCCATCTTCCTCATGCCATCTGGAACAATTGGC
EST: gi|71311670|gb|DR792243.1|DR792243
EST:     AGCACACTCTTGATATCAAAGAATGGGAAAGCGAGGCTGAGTATGAGTAT                         GTGAAACGTAATGGTGTGTCCATCTTCCTCATGCCATCTGGAACAATTGGC
genomic: AGCACACTCTTGATATCAAAGAATGGGAAAGCGAGGCTGAGTATGAGTATgtaagtgttc ... ctgaaaatagGTGAAACGTAATGGTGTGTCCATCTTCCTCATGCCATCTGGAACAATTGGC

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), 49 (downstream exon)
Score: 163

ATTTGCAACACCATACAGAGTTACATGGGATTACTACTTTCTGGGGCGAGAGCACACTCTTGATATCAAAGAATGGGAAAGCGAGGCTGAGTATGAGTATgtaagtgttc ... ctgaaaatagGTGAAACGTAATGGTGTGTCCATCTTCCTCATGCCATCTGGAACAATTGGCACACTTCGAGCACTCTGGGATGTCTTCCCTCTGTTCACAAATACTGCAT


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 330

ATTTGCAACACCATACAGAGTTACATGGGATTACTACTTTCTGGGGCGAGAGCACACTCTTGATATCAAAGAATGGGAAAGCGAGGCTGAGTATGAGTATgtaagtgttc ... ctgaaaatagGTGAAACGTAATGGTGTGTCCATCTTCCTCATGCCATCTGGAACAATTGGCACACTTCGAGCACTCTGGGATGTCTTCCCTCTGTTCACAAATACTGCAT


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

ATTTGCAACACCATACAGAGTTACATGGGATTACTACTTTCTGGGGCGAGAGCACACTCTTGATATCAAAGAATGGGAAAGCGAGGCTGAGTATGAGTATgtaagtgttc ... ctgaaaatagGTGAAACGTAATGGTGTGTCCATCTTCCTCATGCCATCTGGAACAATTGGCACACTTCGAGCACTCTGGGATGTCTTCCCTCTGTTCACAAATACTGCAT


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 410

ATTTGCAACACCATACAGAGTTACATGGGATTACTACTTTCTGGGGCGAGAGCACACTCTTGATATCAAAGAATGGGAAAGCGAGGCTGAGTATGAGTATgtaagtgttc ... ctgaaaatagGTGAAACGTAATGGTGTGTCCATCTTCCTCATGCCATCTGGAACAATTGGCACACTTCGAGCACTCTGGGATGTCTTCCCTCTGTTCACAAATACTGCAT




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttatttattcaatccatagctgatacaaattttctaccctgttacctgaaaatagGTGAAACGTAATGGTGTGTCCATCTTCCTCATGCCATCTGGAACAATTGGCACACTTCGAGCACTCTGGGATGTCTTCCCTCTGTTCACAAATACTGCAT
                 agctgat  putative branch site (score: 410)
                      atacaaattttcta  TA-rich tract