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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gcaagtgctgcagatgttctattgtgaactacaatctatgaactttataaagcatcgaaaaccaagtcaatttttttagtttctaatttctgctacttagGATATTTCAATGGTTTTAAGCACCAAGGAGCATCACGAAATCATGGAGAACCTTTCTATCAAGTGTTCTGCTTATTGTTCTATTCTTCCATCTGTCACTA

Basic information

species Zea mays
transcript GRMZM2G460078_T02
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G460078_T03 (Zea mays), 3'ss of exon 3
lower sequence: LOC_Os01g55590.1 (Oryza sativa), 3'ss of exon 3
gcaagtgc--tgcagatgttctattgtg-aactaca-atctatgaactttataaagcatcgaaaaccaagtcaatttttttagtttctaatttctgctactt--agGATATTTCAATGGTTTTAAGCACCAAGGAGCATCACGAAATCATGGAGAACCTTTCTATCAAGTGTTCTGCTTATTGTTCTATTCTTCCATCTGTCACTA
 ||| | |   |   |  || | ||||  ||   || |  | || | ||||  |   ||    ||  | |||     |||||  |||||| | |||  || |  |||| |||||  || |||||||||||||||||||||| || |||||||||||  | |||| ||| ||||||||| | |||||| ||||||||||||| || |
-caaatacaaagtcaacatttttttgtacaagggcatacatttgcaatttactataaattttgaaatatgtc---cctttta--ttctaactgctgaaacctatagGACATTTCGCTGATTTTAAGCACCAAGGAGCATCAAGACATCATGGAGAATATCTCTACCAAATGTTCTGCTCACTGTTCTCTTCTTCCATCTGTGACAA
















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|78111750|gb|DV530147.1|DV530147
EST:     TTGCCCTTAGCTATCCAGAAGCTGAGCTTCTTCATGTCATGAATGACTCA                         GATATTTCAATGGTTTTAAGCACCAAGGAGCATCACGAAATCATGGAGAAC
genomic: TTGCCCTTAGCTATCCAGAAGCTGAGCTTCTTCATGTCATGAATGACTCAgtatgttcca ... tgctacttagGATATTTCAATGGTTTTAAGCACCAAGGAGCATCACGAAATCATGGAGAAC
EST: gi|91049611|gb|EB160029.1|EB160029
EST:     TTGCCCTTAGCTATCCAGAAGCTGAGCTTCTTCATGTCATGAATGACTCA                         GATATTTCAATGGTTTTAAGCACCAAGGAGCATCACGAAATCATGGAGAAC
genomic: TTGCCCTTAGCTATCCAGAAGCTGAGCTTCTTCATGTCATGAATGACTCAgtatgttcca ... tgctacttagGATATTTCAATGGTTTTAAGCACCAAGGAGCATCACGAAATCATGGAGAAC
EST: gi|211025828|gb|FK982703.1|FK982703
EST:     TTGCCCTTAGCTATCCAGAAGCTGAGCTTCTTCATGTCATGAATGACTCA                         GATATTTCAATGGTTTTAAGCAC
genomic: TTGCCCTTAGCTATCCAGAAGCTGAGCTTCTTCATGTCATGAATGACTCAgtatgttcca ... tgctacttagGATATTTCAATGGTTTTAAGCAC
EST: gi|211025826|gb|FK982701.1|FK982701
EST:     TTGCCCTTAGCTATCCAGAAGCTGAGCTTCTTCATGTCATGAATGACTCA                         GATATTTCAATGGTTTTAAGCACCAAGGAGCATCACGAAATCATGGAGAAC
genomic: TTGCCCTTAGCTATCCAGAAGCTGAGCTTCTTCATGTCATGAATGACTCAgtatgttcca ... tgctacttagGATATTTCAATGGTTTTAAGCACCAAGGAGCATCACGAAATCATGGAGAAC
EST: gi|71434528|gb|DR815578.1|DR815578
EST:     TTGCCCTTAGCTATCCAGAAGCTGAGCTTCTTCATGTCATGAATGACTCA                         GATATTTCAATGGTTTTAAGCACCAAGGAGCATCACGAAATCATGGAGAAC
genomic: TTGCCCTTAGCTATCCAGAAGCTGAGCTTCTTCATGTCATGAATGACTCAgtatgttcca ... tgctacttagGATATTTCAATGGTTTTAAGCACCAAGGAGCATCACGAAATCATGGAGAAC
EST: gi|71332183|gb|DR803010.1|DR803010
EST:     TTGCCCTTAGCTATCCAGAAGCTGAGCTTCTTCATGTCATGAATGACTCA                         GATATTTCAATGGTTTTAAGCACCAAGGAGCATCACGAAATCATGGAGAAC
genomic: TTGCCCTTAGCTATCCAGAAGCTGAGCTTCTTCATGTCATGAATGACTCAgtatgttcca ... tgctacttagGATATTTCAATGGTTTTAAGCACCAAGGAGCATCACGAAATCATGGAGAAC
EST: gi|93012882|gb|EB638402.1|EB638402
EST:     TTGCCCTTAGCTATCCAGAAGCTGAGCTTCTTCATGTCATGAATGACTCA                         GATATTTCAATGGTTTTAAGCACCAAGGAGCATCACGAAATCATGGAGAAC
genomic: TTGCCCTTAGCTATCCAGAAGCTGAGCTTCTTCATGTCATGAATGACTCAgtatgttcca ... tgctacttagGATATTTCAATGGTTTTAAGCACCAAGGAGCATCACGAAATCATGGAGAAC
EST: gi|148961982|gb|EE012780.2|EE012780
EST:     TTGCCCTTAGCTATCCAGAAGCTGAGCTTCTTCATGTCATGAATGACTCA                         GATATTTCAATGGTTTTAAGCACCAAGGAGCATCACGAAATCATGGAGAAC
genomic: TTGCCCTTAGCTATCCAGAAGCTGAGCTTCTTCATGTCATGAATGACTCAgtatgttcca ... tgctacttagGATATTTCAATGGTTTTAAGCACCAAGGAGCATCACGAAATCATGGAGAAC
EST: gi|24766847|gb|CA401979.1|CA401979
EST:     TTGCCCTTAGCTATCCAGAAGCTGAGCTTCTTCATGTCATGAATGACTCA                         GATATTTCAATGGGTGGGGGCACCAAGGAGCATCACGAAATCATGGAGAAC
genomic: TTGCCCTTAGCTATCCAGAAGCTGAGCTTCTTCATGTCATGAATGACTCAgtatgttcca ... tgctacttagGATATTTCAATGGTTTTAAGCACCAAGGAGCATCACGAAATCATGGAGAAC
EST: gi|76925597|gb|DV170498.1|DV170498
EST:     TTGCCCTTAGCTATCCAGAAGCTGAGCTTCTTCATGTCATGAATGACTCA                         GATATTTCAATGGTTTTAAGCACCAAGGAGCATCACGAAATCATGGAGAAC
genomic: TTGCCCTTAGCTATCCAGAAGCTGAGCTTCTTCATGTCATGAATGACTCAgtatgttcca ... tgctacttagGATATTTCAATGGTTTTAAGCACCAAGGAGCATCACGAAATCATGGAGAAC

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: 86

TGTTGCTGGGGTATTTGGAACCTGGCTTTCTGGTGGAGTTGCAGTACCCCTTGCCCTTAGCTATCCAGAAGCTGAGCTTCTTCATGTCATGAATGACTCAgtatgttcca ... tgctacttagGATATTTCAATGGTTTTAAGCACCAAGGAGCATCACGAAATCATGGAGAACCTTTCTATCAAGTGTTCTGCTTATTGTTCTATTCTTCCATCTGTCACTA


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 184

TGTTGCTGGGGTATTTGGAACCTGGCTTTCTGGTGGAGTTGCAGTACCCCTTGCCCTTAGCTATCCAGAAGCTGAGCTTCTTCATGTCATGAATGACTCAgtatgttcca ... tgctacttagGATATTTCAATGGTTTTAAGCACCAAGGAGCATCACGAAATCATGGAGAACCTTTCTATCAAGTGTTCTGCTTATTGTTCTATTCTTCCATCTGTCACTA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 136

TGTTGCTGGGGTATTTGGAACCTGGCTTTCTGGTGGAGTTGCAGTACCCCTTGCCCTTAGCTATCCAGAAGCTGAGCTTCTTCATGTCATGAATGACTCAgtatgttcca ... tgctacttagGATATTTCAATGGTTTTAAGCACCAAGGAGCATCACGAAATCATGGAGAACCTTTCTATCAAGTGTTCTGCTTATTGTTCTATTCTTCCATCTGTCACTA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 475

TGTTGCTGGGGTATTTGGAACCTGGCTTTCTGGTGGAGTTGCAGTACCCCTTGCCCTTAGCTATCCAGAAGCTGAGCTTCTTCATGTCATGAATGACTCAgtatgttcca ... tgctacttagGATATTTCAATGGTTTTAAGCACCAAGGAGCATCACGAAATCATGGAGAACCTTTCTATCAAGTGTTCTGCTTATTGTTCTATTCTTCCATCTGTCACTA




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tataaagcatcgaaaaccaagtcaatttttttagtttctaatttctgctacttagGATATTTCAATGGTTTTAAGCACCAAGGAGCATCACGAAATCATGGAGAACCTTTCTATCAAGTGTTCTGCTTATTGTTCTATTCTTCCATCTGTCACTA
                                   ttctaat  putative branch site (score: 475)
                                         tttctgct  CT-rich tract
                     tcaatttttttagttt  TA-rich tract