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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtactgtcacgactaacatattcccatgttttttaccagcacaaactttgattactaaagctatttattatctttatgaatgaatttgctcacttatctagGTCGAGATGGGTGGCTGCAAAGCTCCAATTACAACCTTCATAGTTGAACCATTTGTGCCACATGACCAAGAGTACTACCTTTCGATTGTATCTGAAAGGC

Basic information

species Zea mays
transcript GRMZM2G034083_T01
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G034083_T01 (Zea mays), 3'ss of exon 2
lower sequence: LOC_Os12g37870.1 (Oryza sativa), 3'ss of exon 2
gtactgtcacgacta-acatattcccatgttttttaccagcacaaactttgattactaaagctatttattatctttatgaatgaatttgctcacttatctagGTCGAGATGGGTGGCTGCAAAGCTCCAATTACAACCTTCATAGTTGAACCATTTGTGCCACATGACCAAGAGTACTACCTTTCGATTGTATCTGAAAGGC
             || |||| |||||||| |||    |     |||| ||| |   || | |||||  | | || |  |      | |||    ||||  |||| ||||||||||||||||| ||||| |||||||| ||||||||||| |||||||| |||||||| ||||||||||| ||||| |||||||| || ||||
--------gtagttatacattttcccatgctttgcctcta---aaaccttgttagttataactattc-taagctatccgg-----tatgcctg-ttatgcagGTTGAGATGGGTGGCTGCAAGGCTCCTATTACAACATTCATAGTTGAGCCATTTGTTCCACATGATCAAGAGTACTATCTTTCTATTGTATCAGAGAGGC

upper sequence: GRMZM2G034083_T01 (Zea mays), 3'ss of exon 2
lower sequence: Vv14s0060g00550.t01 (Vitis vinifera), 3'ss of exon 2
gtactgtcacgactaacatattcccatgttttttaccagcacaaactttgattactaaagctatttattatctttatgaatgaatttgctcacttatctagGTCGAGATGGGTGGCTGCAAAGCTCCAATTACAACCTTCATAGTTGAACCATTTGTGCCACATGACCAAGAGTACTACCTTTCGATTGTATCTGAAAGGC
                 ||     |||    ||||||||    || ||||   |||||     |   || | || |    |||||| | |    | | ||||| ||||||||||| ||||| || ||||| || || || || |||||||| ||||| || |||||||||||||| |||||||||||||||||||| ||||
--------------gtgatgaatgcatcaaatttaccag----aattttggc-actaa----ttcatttctgttaacatgtgaattggatt--ctctttagGTTGAGATGGGTGGTTGCAAGGCACCAATAACCACTTTTATTGTTGAACCGTTTGTTCCCCATGACCAAGAGTATTACCTTTCGATTGTATCTGATAGGC
















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|32849716|gb|CD989397.1|CD989397
EST:     TAGATCTTGCCCAAGTTCGCCAATTTGTCAAGGAGCGGTTGGGAGTTGAG                         GTCGAGATGGGTGGCTGCAAAGCTCCAATTACAACCTTCATAGTTGAACCA
genomic: TAGATCTTGCCCAAGTTCGCCAATTTGTCAAGGAGCGGTTGGGAGTTGAGgtactgtcac ... acttatctagGTCGAGATGGGTGGCTGCAAAGCTCCAATTACAACCTTCATAGTTGAACCA
EST: gi|31356652|gb|CD441009.1|CD441009
EST:     TAGATCTTGCCCAAGTTCGCCAATTTGTCAAGGAGCGGTTGGGAGTTGAG                         GTCGAGATGGGTGGCTGCAAAGCTCCAATTACAACCTTCATAGTTGAACCA
genomic: TAGATCTTGCCCAAGTTCGCCAATTTGTCAAGGAGCGGTTGGGAGTTGAGgtactgtcac ... acttatctagGTCGAGATGGGTGGCTGCAAAGCTCCAATTACAACCTTCATAGTTGAACCA
EST: gi|32927225|gb|CF032037.1|CF032037
EST:     TAGATCTTGCCCAAGTTCGCCAATTTGTCAAGGAGCGGTTGGGAGTTGAG                         GTCGAGATGGGTGGCTGCAAAGCTCCAATTACAACCTTCATAGTTGAACCA
genomic: TAGATCTTGCCCAAGTTCGCCAATTTGTCAAGGAGCGGTTGGGAGTTGAGgtactgtcac ... acttatctagGTCGAGATGGGTGGCTGCAAAGCTCCAATTACAACCTTCATAGTTGAACCA
EST: gi|37416539|gb|CF645921.1|CF645921
EST:     TANATCTTGCCCAAGTTCGCCAATTTGTCAAGGAGCGGTTGGGAGTTGAG                         GTCNAGATGGGTGGCTGCAAAGCTCCAATTA
genomic: TAGATCTTGCCCAAGTTCGCCAATTTGTCAAGGAGCGGTTGGGAGTTGAGgtactgtcac ... acttatctagGTCGAGATGGGTGGCTGCAAAGCTCCAATTA
EST: gi|26558189|gb|CA830424.1|CA830424
EST:     TAGATCTTGCCCAAGTTCGCCAATTTGTCAAGGAGCGGTTGGGAGTTGAG                         GTCGAGATGGGTGGCTGCAAAGCTCCAATTACAACCTTCATAGTTGAGCCA
genomic: TAGATCTTGCCCAAGTTCGCCAATTTGTCAAGGAGCGGTTGGGAGTTGAGgtactgtcac ... acttatctagGTCGAGATGGGTGGCTGCAAAGCTCCAATTACAACCTTCATAGTTGAACCA
EST: gi|21987306|gb|BQ778834.1|BQ778834
EST:     TAGATCTTGCCCAAGTTCGCCAATTTGTCAAGGAGCGGTTGGGAGTTGAG                         GTCGAGATGGGTGGCTGCAAAGCTCCAATTACAACCTTCATAGTTGAGCCA
genomic: TAGATCTTGCCCAAGTTCGCCAATTTGTCAAGGAGCGGTTGGGAGTTGAGgtactgtcac ... acttatctagGTCGAGATGGGTGGCTGCAAAGCTCCAATTACAACCTTCATAGTTGAACCA
EST: gi|149008523|gb|EE040696.2|EE040696
EST:     TAGATCTTGCCCAAGTTCGCCAATTTGTCAAGGAGCGGTTGGGAGTTGAG                         GTCGAGATGGGTGGCTGCAAAGCTCCAATTACAACCTTCATAGTTGAACCA
genomic: TAGATCTTGCCCAAGTTCGCCAATTTGTCAAGGAGCGGTTGGGAGTTGAGgtactgtcac ... acttatctagGTCGAGATGGGTGGCTGCAAAGCTCCAATTACAACCTTCATAGTTGAACCA
EST: gi|67010398|gb|CO439147.1|CO439147
EST:     TAGATCTTGCCCAAGTTCGCCAATTTGTCAAGGAGCGGTTGGGAGTTGAG                         GTCGAGATGGGTGGCTGCAAAGCTCCAATTACAACCTTCATAGTTGAACCA
genomic: TAGATCTTGCCCAAGTTCGCCAATTTGTCAAGGAGCGGTTGGGAGTTGAGgtactgtcac ... acttatctagGTCGAGATGGGTGGCTGCAAAGCTCCAATTACAACCTTCATAGTTGAACCA
EST: gi|149000525|gb|EE037708.2|EE037708
EST:     TAGATCTTGCCCAAGTTCGCCAATTTGTCAAGGAGCGGTTGGGAGTTGAG                         GTCGAGATGGGTGGCTGCAAAGCTCCAATTACAACCTTCATAGTTGAACCA
genomic: TAGATCTTGCCCAAGTTCGCCAATTTGTCAAGGAGCGGTTGGGAGTTGAGgtactgtcac ... acttatctagGTCGAGATGGGTGGCTGCAAAGCTCCAATTACAACCTTCATAGTTGAACCA
EST: gi|211020099|gb|FL063972.1|FL063972
EST:     TAGATCTTGCCCAAGTTCGCCAATTTGTCAAGGAGCGGTTGGGAGTTGAG                         GTCGAGATGGGTGGCTGCAAAGCTCCAATTACAACCTTCATAGTTGAACCA
genomic: TAGATCTTGCCCAAGTTCGCCAATTTGTCAAGGAGCGGTTGGGAGTTGAGgtactgtcac ... acttatctagGTCGAGATGGGTGGCTGCAAAGCTCCAATTACAACCTTCATAGTTGAACCA
EST: gi|148951643|gb|EC897387.2|EC897387
EST:     TAGATCTTGCCCAAGTTCGCCAATTTGTCAAGGAGCGGTTGGGAGTTGAG                         GTCGAGATGGGTGGCTGCAAAGCTCCAATTACAACCTTCATAGTTGAACCA
genomic: TAGATCTTGCCCAAGTTCGCCAATTTGTCAAGGAGCGGTTGGGAGTTGAGgtactgtcac ... acttatctagGTCGAGATGGGTGGCTGCAAAGCTCCAATTACAACCTTCATAGTTGAACCA
EST: gi|149110454|gb|EE190425.2|EE190425
EST:     TAGATCTTGCCCAAGTTCGCCAATTTGTCAAGGAGCGGTTGGGAGTTGAG                         GTCGAGATGGGTGGCTGCAAAGCTCCAATTACAACCTTCATAGTTGAACCA
genomic: TAGATCTTGCCCAAGTTCGCCAATTTGTCAAGGAGCGGTTGGGAGTTGAGgtactgtcac ... acttatctagGTCGAGATGGGTGGCTGCAAAGCTCCAATTACAACCTTCATAGTTGAACCA
EST: gi|78103681|gb|DV522109.1|DV522109
EST:     TAGATCTTGCCCAAGTTCGCCAATTTGTCAAGGAGCGGTTGGGAGTTGAG                         GTCGAGATGGGTGGCTGCAAAGCTCCAATTACAACCTTCATAGTTGAACCA
genomic: TAGATCTTGCCCAAGTTCGCCAATTTGTCAAGGAGCGGTTGGGAGTTGAGgtactgtcac ... acttatctagGTCGAGATGGGTGGCTGCAAAGCTCCAATTACAACCTTCATAGTTGAACCA
EST: gi|211020096|gb|FL063969.1|FL063969
EST:     TAGATCTTGCCCAAGTTCGCCAATTTGTCAAGGAGCGGTTGGGAGTTGAG                         GTCGAGATGGGTGGCTGCAAAGCTCCAATTACAACCTTCATAGTTGAACCA
genomic: TAGATCTTGCCCAAGTTCGCCAATTTGTCAAGGAGCGGTTGGGAGTTGAGgtactgtcac ... acttatctagGTCGAGATGGGTGGCTGCAAAGCTCCAATTACAACCTTCATAGTTGAACCA
EST: gi|149070778|gb|EE159189.2|EE159189
EST:     TAGATCTTGCCCAAGTTCGCCAATTTGTCAAGGAGCGGTTGGGAGTTGAG                         GTCGAGATGGGTGGCTGCAAAGCTCCAATTACAACCTTCATAGTTGAACCA
genomic: TAGATCTTGCCCAAGTTCGCCAATTTGTCAAGGAGCGGTTGGGAGTTGAGgtactgtcac ... acttatctagGTCGAGATGGGTGGCTGCAAAGCTCCAATTACAACCTTCATAGTTGAACCA
EST: gi|13381841|gb|BG458516.1|BG458516
EST:     GCCAATTTGTCAAGGAGCGGTTGGGAGTTGAG                         GTCGAGATGGGTGGCTGCAAAGCTCCAATTACAACCTTCATAGTTGAACCA
genomic: GCCAATTTGTCAAGGAGCGGTTGGGAGTTGAGgtactgtcac ... acttatctagGTCGAGATGGGTGGCTGCAAAGCTCCAATTACAACCTTCATAGTTGAACCA
EST: gi|13150055|gb|BG320377.1|BG320377
EST:     TAGATCTTGCCCAAGTTCGCCAATTTGTCAAGGAGCGGTTGGGAGTTGAG                         GTCGAGATGGGTGGCTGCAAAGCTCCAATTACAACCTTCATAGTTGAACCA
genomic: TAGATCTTGCCCAAGTTCGCCAATTTGTCAAGGAGCGGTTGGGAGTTGAGgtactgtcac ... acttatctagGTCGAGATGGGTGGCTGCAAAGCTCCAATTACAACCTTCATAGTTGAACCA
EST: gi|211133983|gb|FL063982.1|FL063982
EST:     TAGATCTTGCCCAAGTTCGCCAATTTGTCAAGGAGCGGTTGGGAGTTGAG                         GTCGAGATGGGTGGCTGCAAAGCTCCAATTACAACCTTCATAGTTGAACCA
genomic: TAGATCTTGCCCAAGTTCGCCAATTTGTCAAGGAGCGGTTGGGAGTTGAGgtactgtcac ... acttatctagGTCGAGATGGGTGGCTGCAAAGCTCCAATTACAACCTTCATAGTTGAACCA
EST: gi|148947869|gb|EC893362.2|EC893362
EST:     TAGATCTTGCCCAAGTTCGCCAATTTGTCAAGGAGCGGTTGGGAGTTGAG                         GTCGAGATGGGTGGCTGCAAAGCTCCAATTACAACCTTCATAGTTGAACCA
genomic: TAGATCTTGCCCAAGTTCGCCAATTTGTCAAGGAGCGGTTGGGAGTTGAGgtactgtcac ... acttatctagGTCGAGATGGGTGGCTGCAAAGCTCCAATTACAACCTTCATAGTTGAACCA
EST: gi|211020104|gb|FL063977.1|FL063977
EST:     TAGATCTTGMC-AAGTTCGCCAATTTGTCAAGGAGCGGTTGGGAGTTGAG                         GTCGAGATGGGTGGCTGCAAAS-TCCAATTACAACCTTCATAGTTGAACCA
genomic: TAGATCTTGCCCAAGTTCGCCAATTTGTCAAGGAGCGGTTGGGAGTTGAGgtactgtcac ... acttatctagGTCGAGATGGGTGGCTGCAAAGCTCCAATTACAACCTTCATAGTTGAACCA
EST: gi|31355046|gb|CD439403.1|CD439403
EST:     TAGATCTTGCCCAAGTTCGCCAATTTGTCAAGGAGCGGTTGGGAGTTGAG                         GTCGAGATGGGTGGCTGCAAAGCTCCAATTACAACCTTCATAGTTGAACCA
genomic: TAGATCTTGCCCAAGTTCGCCAATTTGTCAAGGAGCGGTTGGGAGTTGAGgtactgtcac ... acttatctagGTCGAGATGGGTGGCTGCAAAGCTCCAATTACAACCTTCATAGTTGAACCA
EST: gi|148935016|gb|EC879057.2|EC879057
EST:     TAGATCTTGCCCAAGTTCGCCAATTTGTCAAGGAGCGGTTGGGAGTTGAG                         GTCGAGATGGGTGGCTGCAAAGCTCCAATTACAACCTTCATAGTTGAACCA
genomic: TAGATCTTGCCCAAGTTCGCCAATTTGTCAAGGAGCGGTTGGGAGTTGAGgtactgtcac ... acttatctagGTCGAGATGGGTGGCTGCAAAGCTCCAATTACAACCTTCATAGTTGAACCA
EST: gi|211020100|gb|FL063973.1|FL063973
EST:     TAGATCTTGCCCAAGTTCGCCAATTTGTCAAGGAGCGGTTGGGAGTTGAG                         GTCGAGATGGGTGGCTGCAAAGCTCCAATTACAACCTTCATAGTTGAACCA
genomic: TAGATCTTGCCCAAGTTCGCCAATTTGTCAAGGAGCGGTTGGGAGTTGAGgtactgtcac ... acttatctagGTCGAGATGGGTGGCTGCAAAGCTCCAATTACAACCTTCATAGTTGAACCA
EST: gi|148958422|gb|EC904655.2|EC904655
EST:     TAGATCTTGCCCAAGTTCGCCAATTTGTCAAGGAGCGGTTGGGAGTTGAG                         GTCGAGATGGGTGGCTGCAAAGCTCCAATTACAACCTTCATAGTTGAACCA
genomic: TAGATCTTGCCCAAGTTCGCCAATTTGTCAAGGAGCGGTTGGGAGTTGAGgtactgtcac ... acttatctagGTCGAGATGGGTGGCTGCAAAGCTCCAATTACAACCTTCATAGTTGAACCA
EST: gi|9566469|gb|BE475978.1|BE475978
EST:     TAGATCTTGCCCAAGTTCGCCAATTTGTCAAGGAGCGGTTGGGAGTTGAG                         GTCGAGATGGGTGGCTGCAAAGCTCCAATTACAACCTTCATAGTTGAGCCA
genomic: TAGATCTTGCCCAAGTTCGCCAATTTGTCAAGGAGCGGTTGGGAGTTGAGgtactgtcac ... acttatctagGTCGAGATGGGTGGCTGCAAAGCTCCAATTACAACCTTCATAGTTGAACCA
EST: gi|149113031|gb|EE295802.2|EE295802
EST:     TAGATCTTGCCCAAGTTCGCCAATTTGTCAAGGAGCGGTTGGGAGTTGAG                         GTCGAGATGGGTGGCTGCAAAGCTCCAATTACAACCTTCATAGTTGAACCA
genomic: TAGATCTTGCCCAAGTTCGCCAATTTGTCAAGGAGCGGTTGGGAGTTGAGgtactgtcac ... acttatctagGTCGAGATGGGTGGCTGCAAAGCTCCAATTACAACCTTCATAGTTGAACCA
EST: gi|148955951|gb|EC901669.2|EC901669
EST:     TAGATCTTGCCCAAGTTCGCCAATTTGTCAAGGAGCGGTTGGGAGTTGAG                         GTCGAGATGGGTGGCTGCAAAGCTCCAATTACAACCTTCATAGTTGAACCA
genomic: TAGATCTTGCCCAAGTTCGCCAATTTGTCAAGGAGCGGTTGGGAGTTGAGgtactgtcac ... acttatctagGTCGAGATGGGTGGCTGCAAAGCTCCAATTACAACCTTCATAGTTGAACCA
EST: gi|148957836|gb|EC903982.2|EC903982
EST:     TAGATCTTGCCCAAGTTCGCCAATTTGTCAAGGAGCGGTTGGGAGTTGAC                         GTCCAGATGGGTGGCTGCAAAGCTTCCA-TTACACCCTT
genomic: TAGATCTTGCCCAAGTTCGCCAATTTGTCAAGGAGCGGTTGGGAGTTGAGgtactgtcac ... acttatctagGTCGAGATGGGTGGCTGCAAAGCT-CCAATTACAACCTT
EST: gi|148986293|gb|EE030028.2|EE030028
EST:     TAGATCTTGCCCAAGTTCGCCAATTTGTCAAGGAGCGGTTGGGAGTTGAG                         GTCGAGATGGGTGGCTGCAAAGCTCCAATTACAACCTTCATAGTTGAACCA
genomic: TAGATCTTGCCCAAGTTCGCCAATTTGTCAAGGAGCGGTTGGGAGTTGAGgtactgtcac ... acttatctagGTCGAGATGGGTGGCTGCAAAGCTCCAATTACAACCTTCATAGTTGAACCA

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: 340

TGACATGCTCTTTGGGAAACGTGGGAAGAGTGGGCTTGTGGCCCTCAACCTAGATCTTGCCCAAGTTCGCCAATTTGTCAAGGAGCGGTTGGGAGTTGAGgtactgtcac ... acttatctagGTCGAGATGGGTGGCTGCAAAGCTCCAATTACAACCTTCATAGTTGAACCATTTGTGCCACATGACCAAGAGTACTACCTTTCGATTGTATCTGAAAGGC


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 840

TGACATGCTCTTTGGGAAACGTGGGAAGAGTGGGCTTGTGGCCCTCAACCTAGATCTTGCCCAAGTTCGCCAATTTGTCAAGGAGCGGTTGGGAGTTGAGgtactgtcac ... acttatctagGTCGAGATGGGTGGCTGCAAAGCTCCAATTACAACCTTCATAGTTGAACCATTTGTGCCACATGACCAAGAGTACTACCTTTCGATTGTATCTGAAAGGC


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 599

TGACATGCTCTTTGGGAAACGTGGGAAGAGTGGGCTTGTGGCCCTCAACCTAGATCTTGCCCAAGTTCGCCAATTTGTCAAGGAGCGGTTGGGAGTTGAGgtactgtcac ... acttatctagGTCGAGATGGGTGGCTGCAAAGCTCCAATTACAACCTTCATAGTTGAACCATTTGTGCCACATGACCAAGAGTACTACCTTTCGATTGTATCTGAAAGGC


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 1214

TGACATGCTCTTTGGGAAACGTGGGAAGAGTGGGCTTGTGGCCCTCAACCTAGATCTTGCCCAAGTTCGCCAATTTGTCAAGGAGCGGTTGGGAGTTGAGgtactgtcac ... acttatctagGTCGAGATGGGTGGCTGCAAAGCTCCAATTACAACCTTCATAGTTGAACCATTTGTGCCACATGACCAAGAGTACTACCTTTCGATTGTATCTGAAAGGC




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tttgattactaaagctatttattatctttatgaatgaatttgctcacttatctagGTCGAGATGGGTGGCTGCAAAGCTCCAATTACAACCTTCATAGTTGAACCATTTGTGCCACATGACCAAGAGTACTACCTTTCGATTGTATCTGAAAGGC
                                          ctcactt  CT-rich tract
               tatttattatctttat  TA-rich tract