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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TCCTCCCTCCCTCTCGATCTGATCCGGAGTGGCTCACGTTTTCCTATTCCTCGCCAGCGGCAGAGGCGGCAACCCTCGATCCGTGTCAATCCTCTATTAGgtacgtcacccgtttcgtggaaccgaccaacccaagctatattgcatcaggaactgacccggtggctagtattggtagtatattcatgtttttagacctt...

Basic information

species Zea mays
transcript GRMZM2G109651_T03
intron # 1
splice site 5'
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|211512441|gb|FL330196.1|FL330196
EST:     TCGCCAGCGGCAGAGGCGGCAACCCTCGATCCGTGTCAATCCTCTATTAG                         ATTGGTATGAGCTGATCACCCCTGGTTGTGTAGTTCCTTCTGCAATGATTT
genomic: TCGCCAGCGGCAGAGGCGGCAACCCTCGATCCGTGTCAATCCTCTATTAGgtacgtcacc ... agtttcacagATTGGTATGAGCTGATCACCCCTGGTTGTGTAGTTCCTTCTGCAATGATTT
EST: gi|76018273|gb|DT945443.1|DT945443
EST:     TCGCCAGCGGCAGAGGCGGCAACCCTCGATCCGTGTCAATCCTCTATTAG                         T
genomic: TCGCCAGCGGCAGAGGCGGCAACCCTCGATCCGTGTCAATCCTCTATTAGgtacgtcacc ... agtttcacag-
EST: gi|76018273|gb|DT945443.1|DT945443
EST:     TCGCCAGCGGCAGAGGCGGCAACCCTCGATCCGTGTCAATCCTCTATTAG                         T
genomic: TCGCCAGCGGCAGAGGCGGCAACCCTCGATCCGTGTCAATCCTCTATTAGgtacgtcacc ... agtttcacag-
EST: gi|76018273|gb|DT945443.1|DT945443
EST:     TCGCCAGCGGCAGAGGCGGCAACCCTCGATCCGTGTCAATCCTCTATTAG                         T
genomic: TCGCCAGCGGCAGAGGCGGCAACCCTCGATCCGTGTCAATCCTCTATTAGgtacgtcacc ... agtttcacag-
EST: gi|76018273|gb|DT945443.1|DT945443
EST:     TCGCCAGCGGCAGAGGCGGCAACCCTCGATCCGTGTCAATCCTCTATTAG                         T
genomic: TCGCCAGCGGCAGAGGCGGCAACCCTCGATCCGTGTCAATCCTCTATTAGgtacgtcacc ... agtttcacag-
EST: gi|76018273|gb|DT945443.1|DT945443
EST:     TCGCCAGCGGCAGAGGCGGCAACCCTCGATCCGTGTCAATCCTCTATTAG                         T
genomic: TCGCCAGCGGCAGAGGCGGCAACCCTCGATCCGTGTCAATCCTCTATTAGgtacgtcacc ... agtttcacag-
EST: gi|91051140|gb|EB161558.1|EB161558
EST:     TCGCCAGCGGCAGAGGCGGCAACCCTCGATCCGTGTCAATCCTCTATTAG                         ATTGGTATGAGCTGATCACCCCTGGGTGTGTAGTTCCTTCTGCAATGATTT
genomic: TCGCCAGCGGCAGAGGCGGCAACCCTCGATCCGTGTCAATCCTCTATTAGgtacgtcacc ... agtttcacagATTGGTATGAGCTGATCACCCCTGGTTGTGTAGTTCCTTCTGCAATGATTT
EST: gi|93017293|gb|EB642813.1|EB642813
EST:     TCGCCAGCGGCAGAGGCGGCAACCCTCGATCCGTGTCAATCCTCTATTAG                         T
genomic: TCGCCAGCGGCAGAGGCGGCAACCCTCGATCCGTGTCAATCCTCTATTAGgtacgtcacc ... agtttcacag-
EST: gi|93017293|gb|EB642813.1|EB642813
EST:     TCGCCAGCGGCAGAGGCGGCAACCCTCGATCCGTGTCAATCCTCTATTAG                         T
genomic: TCGCCAGCGGCAGAGGCGGCAACCCTCGATCCGTGTCAATCCTCTATTAGgtacgtcacc ... agtttcacag-
EST: gi|93017293|gb|EB642813.1|EB642813
EST:     TCGCCAGCGGCAGAGGCGGCAACCCTCGATCCGTGTCAATCCTCTATTAG                         T
genomic: TCGCCAGCGGCAGAGGCGGCAACCCTCGATCCGTGTCAATCCTCTATTAGgtacgtcacc ... agtttcacag-
EST: gi|93017293|gb|EB642813.1|EB642813
EST:     TCGCCAGCGGCAGAGGCGGCAACCCTCGATCCGTGTCAATCCTCTATTAG                         T
genomic: TCGCCAGCGGCAGAGGCGGCAACCCTCGATCCGTGTCAATCCTCTATTAGgtacgtcacc ... agtttcacag-
EST: gi|93017293|gb|EB642813.1|EB642813
EST:     TCGCCAGCGGCAGAGGCGGCAACCCTCGATCCGTGTCAATCCTCTATTAG                         T
genomic: TCGCCAGCGGCAGAGGCGGCAACCCTCGATCCGTGTCAATCCTCTATTAGgtacgtcacc ... agtttcacag-
EST: gi|78027070|gb|DV495457.1|DV495457
EST:     TCGCCAGCGGCAGAGGCGGCAACCCTCGATCCGTGTCAATCCTCTATTAGTTTCACAG                  
genomic: TCGCCAGCGGCAGAGGCGGCAACCCTCGATCCGTGTCAATCCTC---TA--TT---AGgtacgtcacc ... agt
EST: gi|211495115|gb|FL339938.1|FL339938
EST:     TCGCCAGCGGCAGAGGCGGCAACCCTCGATCCGTGTCAATCCTCTATTAG                         ATTGGTATGAGCTGATCACCCCTGGTTGTGTAGTTTCCTTCTGCAATGATT
genomic: TCGCCAGCGGCAGAGGCGGCAACCCTCGATCCGTGTCAATCCTCTATTAGgtacgtcacc ... agtttcacagATTGGTATGAGCTGATCACCCCTGGTTGTGTAGTT-CCTTCTGCAATGATT

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: 48 (upstream exon), 41 (downstream exon)
Score: 14

TCCTCCCTCCCTCTCGATCTGATCCGGAGTGGCTCACGTTTTCCTATTCCTCGCCAGCGGCAGAGGCGGCAACCCTCGATCCGTGTCAATCCTCTATTAGgtacgtcacc ... agtttcacagATTGGTATGAGCTGATCACCCCTGGTTGTGTAGTTCCTTCTGCAATGATTTACTGCACTCACTGTGCTGATTACTGCCCCTCCATAAAGGACCCTGACAA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 15

TCCTCCCTCCCTCTCGATCTGATCCGGAGTGGCTCACGTTTTCCTATTCCTCGCCAGCGGCAGAGGCGGCAACCCTCGATCCGTGTCAATCCTCTATTAGgtacgtcacc ... agtttcacagATTGGTATGAGCTGATCACCCCTGGTTGTGTAGTTCCTTCTGCAATGATTTACTGCACTCACTGTGCTGATTACTGCCCCTCCATAAAGGACCCTGACAA


Block sizes: 34 (upstream exon), 49 (downstream exon)
Score: 7

TCCTCCCTCCCTCTCGATCTGATCCGGAGTGGCTCACGTTTTCCTATTCCTCGCCAGCGGCAGAGGCGGCAACCCTCGATCCGTGTCAATCCTCTATTAGgtacgtcacc ... agtttcacagATTGGTATGAGCTGATCACCCCTGGTTGTGTAGTTCCTTCTGCAATGATTTACTGCACTCACTGTGCTGATTACTGCCCCTCCATAAAGGACCCTGACAA


Block sizes: 48 (upstream exon), 36 (downstream exon)
Score: 7

TCCTCCCTCCCTCTCGATCTGATCCGGAGTGGCTCACGTTTTCCTATTCCTCGCCAGCGGCAGAGGCGGCAACCCTCGATCCGTGTCAATCCTCTATTAGgtacgtcacc ... agtttcacagATTGGTATGAGCTGATCACCCCTGGTTGTGTAGTTCCTTCTGCAATGATTTACTGCACTCACTGTGCTGATTACTGCCCCTCCATAAAGGACCCTGACAA