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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CTTCCTGGTGTTGATCCCAATGATCCATCTGTTAAAGATTTGCTGGCATCGTTGCACAGCCAGGGAGAGgtatgttctttttcgggtaacactgaaggtccgccagtatttgtgatgcaatgaaattcatgttgcctctagatgatagcattgatcagcttcaccttga...

Basic information

species Zea mays
transcript GRMZM2G165926_T02
intron # 9
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G165926_T02 (Zea mays), 5'ss of exon 9
lower sequence: LOC_Os03g13970.1 (Oryza sativa), 5'ss of exon 9
CTTCCTGGTGTTGATCCCAATGATCCATCTGTTAAAGATTTGCTGGCATCGTTGCACAGCCAGGGAGAGgtatgttctttttcgggtaacactgaaggtccgccagtatttgtgatgcaatgaaattcatgttgcctctagatgatagcattgatcagcttcaccttga----
|| ||||||||||| |||||||| || ||||| ||||||||||||||||| |||||  | ||||| |||||||| | || |     || |  |  || |     ||| |   | |  |   |||  ||    | |   ||    ||   | |    |   || |    |    
CTCCCTGGTGTTGACCCCAATGACCCCTCTGTGAAAGATTTGCTGGCATCATTGCATGGGCAGGGCGAGgtatgcttttctc----tatccttttagattgttgagtttcaatcaaacttagaaggtctgagtacagttatgacattagactttctattgtccctcgtacctt

upper sequence: GRMZM2G165926_T02 (Zea mays), 5'ss of exon 9
lower sequence: GLYMA02G05250.2 (Glycine max), 5'ss of exon 9
CTTCCTGGTGTTGATCCCAATGATCCATCTGTTAAAGATTTGCTGGCATCGTTGCACAGCCAGGGAGAGgtatgttctttttc--gggtaacactga--aggtccgccagtatttgtgatgcaatgaaattcatgttgcctctagatgatagcattgatcagcttcaccttga
|||||||| ||||| || ||||| |||||||| |||||||||||||| ||  |||| |  |||   |||||| ||| | |||   ||  || | | |   |||  | ||  | |  |      | ||  |  |||  | |  |   ||| |  | |  |    |  |  |   
CTTCCTGGGGTTGACCCAAATGACCCATCTGTCAAAGATTTGCTGGCTTCCATGCAAAATCAGTCTGAGgtaggttttcttttatggaaaataatcattgggtttgacaaaaatcttttattgaagatttcaatgggggca-tgtttgacaaaaatctttttttgaagat---

upper sequence: GRMZM2G165926_T02 (Zea mays), 5'ss of exon 9
lower sequence: GLYMA16G23590.1 (Glycine max), 5'ss of exon 9
CTTCCTGGTGTTGATCCCAATGATCCATCTGTTAAAGATTTGCTGGCATCGTTGCACAGCCAGGGAGAGgtatgttctttttcgggtaacac-----tgaaggtccgccagtatttgtgatgcaatgaaattcatgttgcctctagatgatagcattgatcagcttcaccttga
|||||||| ||||| || |||||||||||||| |||||||||||||| || ||||| |  |||   |||||| ||| | |||   | || |      |  || |     || || | | |    ||   |     |     | || ||  |||| |     || ||  ||    
CTTCCTGGGGTTGACCCAAATGATCCATCTGTCAAAGATTTGCTGGCTTCCTTGCAAAATCAGTCTGAGgtaggttttcttttatggaaaataatcattgagtttgaaaagaatctcttagaatatttcacagggggcatatttaaatt-tagcttcacctagattagcc----

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|37380959|gb|CF627330.1|CF627330
EST:     ATGATCCATCTGTTAAAGATTTGCTGGCATCGTTGCACAGCCAGGGAGAG                         CAAGAGAAGAAGGAAGACACGTCAGACAAAACAGAAGACGATAAGAACTGA
genomic: ATGATCCATCTGTTAAAGATTTGCTGGCATCGTTGCACAGCCAGGGAGAGgtatgttctt ... ttttaaacagCAAGAGAAGAAGGAAGACACGTCAGACAAAACAGAAGACGATAAGAACTGA
EST: gi|18162870|gb|BM332709.1|BM332709
EST:     ATGATCCATCTGTTAAAGATTTGCTGGCATCGTTGCACAGCCAGGGAGAG                         CAAGAGAAGAAGGAAGACACGTCAGACAAAACAGAAGACGATAAGAACTGA
genomic: ATGATCCATCTGTTAAAGATTTGCTGGCATCGTTGCACAGCCAGGGAGAGgtatgttctt ... ttttaaacagCAAGAGAAGAAGGAAGACACGTCAGACAAAACAGAAGACGATAAGAACTGA
EST: gi|5525732|gb|AI861625.1|AI861625
EST:     ATGATCCATCTGTTAAAGATTTGCTGGCATCGTTGCACAGCCAGGGAGAG                         CAAGAGAAGAAGGAAGACACGTCAGACAAAACAGAAGACGAGAAGAACTGA
genomic: ATGATCCATCTGTTAAAGATTTGCTGGCATCGTTGCACAGCCAGGGAGAGgtatgttctt ... ttttaaacagCAAGAGAAGAAGGAAGACACGTCAGACAAAACAGAAGACGATAAGAACTGA
EST: gi|71419000|gb|DR804613.1|DR804613
EST:     ATGATCCATCTGTTAAAGATTTGCTGGCATCGTTGCACAGCCAGGGAGAG                         CAAGAGAAGAAGGAAGACACGTCAGACAAAACAGAAGACGATAAGAACTGA
genomic: ATGATCCATCTGTTAAAGATTTGCTGGCATCGTTGCACAGCCAGGGAGAGgtatgttctt ... ttttaaacagCAAGAGAAGAAGGAAGACACGTCAGACAAAACAGAAGACGATAAGAACTGA
EST: gi|37398277|gb|CF636450.1|CF636450
EST:     ATGATCCATCTGTTAAAGATTTGCTGGCATCGTTGCACAGCCAGGGAGAG                         CAAGAGAAGAAGGAAGACACGTCAGACAAAACAGAAGACGATAAGAACTGA
genomic: ATGATCCATCTGTTAAAGATTTGCTGGCATCGTTGCACAGCCAGGGAGAGgtatgttctt ... ttttaaacagCAAGAGAAGAAGGAAGACACGTCAGACAAAACAGAAGACGATAAGAACTGA
EST: gi|60337128|gb|DN204101.1|DN204101
EST:     ATGATCCATCTGTTAAAGATTTGCTGGCATCGTTGCACAGCCAGGGAGAG                         CAAGAGAAGAAGGAAGACACGTCAGACAAAACAGAAGACGATAAGAACTGA
genomic: ATGATCCATCTGTTAAAGATTTGCTGGCATCGTTGCACAGCCAGGGAGAGgtatgttctt ... ttttaaacagCAAGAGAAGAAGGAAGACACGTCAGACAAAACAGAAGACGATAAGAACTGA
EST: gi|60353359|gb|DN220332.1|DN220332
EST:     ATGATCCATCTGTTAAAGATTTGCTGGCATCGTTGCACAGCCAGGGAGAG                         CAAGAGAAGAAGGAAGACACGTCAGACAAAACAGAAGACGATAAGAACTGA
genomic: ATGATCCATCTGTTAAAGATTTGCTGGCATCGTTGCACAGCCAGGGAGAGgtatgttctt ... ttttaaacagCAAGAGAAGAAGGAAGACACGTCAGACAAAACAGAAGACGATAAGAACTGA
EST: gi|60347266|gb|DN214239.1|DN214239
EST:     ATGATCCATCTGTTAAAGATTTGCTGGCATCGTTGCACAGCCAGGGAGAG                         CAAGAGAAGAAGGAAGACACGTCAGACAAAACAGAAGACGATAAGAACTGA
genomic: ATGATCCATCTGTTAAAGATTTGCTGGCATCGTTGCACAGCCAGGGAGAGgtatgttctt ... ttttaaacagCAAGAGAAGAAGGAAGACACGTCAGACAAAACAGAAGACGATAAGAACTGA
EST: gi|37383110|gb|CF628537.1|CF628537
EST:     ATGATCCATCTGTTAAAGATTTGCTGGCATCGTTGCACAGCCAGGGAGAG                         CAAGAGAAGAAGGAAGACACGTCAGACAAAACAGAAGACGATAAGAACTGA
genomic: ATGATCCATCTGTTAAAGATTTGCTGGCATCGTTGCACAGCCAGGGAGAGgtatgttctt ... ttttaaacagCAAGAGAAGAAGGAAGACACGTCAGACAAAACAGAAGACGATAAGAACTGA
EST: gi|31664308|gb|CD573033.1|CD573033
EST:     ATGATCCATCTGTTAAAGATTTGCTGGCATCGTTGCACAGCCAGGGAGAG                         CAAGAGAAGAAGGAAGACCCGTCAGACAAAACAGAAGACGATAAGAACTGA
genomic: ATGATCCATCTGTTAAAGATTTGCTGGCATCGTTGCACAGCCAGGGAGAGgtatgttctt ... ttttaaacagCAAGAGAAGAAGGAAGACACGTCAGACAAAACAGAAGACGATAAGAACTGA
EST: gi|60349443|gb|DN216416.1|DN216416
EST:     ATGATCCATCTGTTAAAGATTTGCTGGCATCGTTGCACAGCCAGGGAGAG                         CAAGAGAAGAAGGAAGACACGTCAGACAAAACAGAAGACGATAAGAACTGA
genomic: ATGATCCATCTGTTAAAGATTTGCTGGCATCGTTGCACAGCCAGGGAGAGgtatgttctt ... ttttaaacagCAAGAGAAGAAGGAAGACACGTCAGACAAAACAGAAGACGATAAGAACTGA
EST: gi|60346958|gb|DN213931.1|DN213931
EST:     ATGATCCATCTGTTAAAGATTTGCTGGCATCGTTGCACAGCCAGGGAGAG                         CAAGAGAAGAAGGAAGACACGTCAGACAAAACAGAAGACGATAAGAACTGA
genomic: ATGATCCATCTGTTAAAGATTTGCTGGCATCGTTGCACAGCCAGGGAGAGgtatgttctt ... ttttaaacagCAAGAGAAGAAGGAAGACACGTCAGACAAAACAGAAGACGATAAGAACTGA
EST: gi|33097806|gb|CF057766.1|CF057766
EST:     ATGATCCATCTGTTAAAGATTTGCTGGCATCGTTGCCCAGCCAGGGAGAG                         CAAGAGAAGAAGGAAGACCCGTCAGACAAAACAGAAGACGAGAAGAACTGA
genomic: ATGATCCATCTGTTAAAGATTTGCTGGCATCGTTGCACAGCCAGGGAGAGgtatgttctt ... ttttaaacagCAAGAGAAGAAGGAAGACACGTCAGACAAAACAGAAGACGATAAGAACTGA
EST: gi|18174967|gb|BM350355.1|BM350355
EST:     ATGATCCATCTGTTAAAGATTTGCTGGCATCGTTGCACAGCCAGGGAGAG                         CAAGAGAAGAAGGAAGACACGTCAGACAAAACAGAAGACGATAAGAACTGA
genomic: ATGATCCATCTGTTAAAGATTTGCTGGCATCGTTGCACAGCCAGGGAGAGgtatgttctt ... ttttaaacagCAAGAGAAGAAGGAAGACACGTCAGACAAAACAGAAGACGATAAGAACTGA
EST: gi|211072583|gb|FL217264.1|FL217264
EST:     ATGATCCATCTGTTAAAGATTTGCTGGCATCGTTGCACAGCCAGGGAGAG                         CAAGAGAAGAAGGAAGACACGTCAGACAAAACAGAAGACGATAAGAACTGA
genomic: ATGATCCATCTGTTAAAGATTTGCTGGCATCGTTGCACAGCCAGGGAGAGgtatgttctt ... ttttaaacagCAAGAGAAGAAGGAAGACACGTCAGACAAAACAGAAGACGATAAGAACTGA
EST: gi|60357544|gb|DN224517.1|DN224517
EST:     ATGATCCATCTGTTAAAGATTTGCTGGCATCGTTGCACAGCCAGGGAGAG                         CAAGAGAAGAAGGAAGACACGTCAGACAAAACAGAAGACGATAAGAACTGA
genomic: ATGATCCATCTGTTAAAGATTTGCTGGCATCGTTGCACAGCCAGGGAGAGgtatgttctt ... ttttaaacagCAAGAGAAGAAGGAAGACACGTCAGACAAAACAGAAGACGATAAGAACTGA
EST: gi|211442872|gb|FL468446.1|FL468446
EST:     ATGATCCATCTGTTAAAGATTTGCTGGCATCGTTGCACAGCCAGGGAGAG                         CAAGAGAAGAAGGAAGACACGTCAGACAAAACAGAAGACGATAAGAACTGA
genomic: ATGATCCATCTGTTAAAGATTTGCTGGCATCGTTGCACAGCCAGGGAGAGgtatgttctt ... ttttaaacagCAAGAGAAGAAGGAAGACACGTCAGACAAAACAGAAGACGATAAGAACTGA
EST: gi|60354620|gb|DN221593.1|DN221593
EST:     ATGATCCATCTGTTAAAGATTTGCTGGCATCGTTGCACAGCCAGGGAGAG                         CAAGAGAAGAAGGAAGACACGTCAGACAAAACAGAAGACGATAAGAACTGA
genomic: ATGATCCATCTGTTAAAGATTTGCTGGCATCGTTGCACAGCCAGGGAGAGgtatgttctt ... ttttaaacagCAAGAGAAGAAGGAAGACACGTCAGACAAAACAGAAGACGATAAGAACTGA
EST: gi|5847367|gb|AW000446.1|AW000446
EST:     ATGATCCATCTGTTAAAGATTTGCTGGCATCGTTGCACAGCCAGGGAGAG                         CAAGAGAAGAAGGAAGACACGTCAGACAAAACAGAAGACGAGAAGAACTGA
genomic: ATGATCCATCTGTTAAAGATTTGCTGGCATCGTTGCACAGCCAGGGAGAGgtatgttctt ... ttttaaacagCAAGAGAAGAAGGAAGACACGTCAGACAAAACAGAAGACGATAAGAACTGA
EST: gi|5706125|gb|AI941901.1|AI941901
EST:     ATGATCCATCTGTTAAAGATTTGCTGGCATCGTTGCACAGCCAGGGAGAG                         CAAGAGAAGAAGGAAGACACGTCAGACAAAACAGAAGACGATAAGAACTGA
genomic: ATGATCCATCTGTTAAAGATTTGCTGGCATCGTTGCACAGCCAGGGAGAGgtatgttctt ... ttttaaacagCAAGAGAAGAAGGAAGACACGTCAGACAAAACAGAAGACGATAAGAACTGA
EST: gi|44901350|gb|CK827895.1|CK827895
EST:     ATGATCCATCTGTTAAAGATTTGCTGGCATCGTTGCACAGCCAGGGAGAG                         CAAGAGAAGAAGGAAGACACGTCAGACAAAACAGAAGACGATAAGAACTGA
genomic: ATGATCCATCTGTTAAAGATTTGCTGGCATCGTTGCACAGCCAGGGAGAGgtatgttctt ... ttttaaacagCAAGAGAAGAAGGAAGACACGTCAGACAAAACAGAAGACGATAAGAACTGA
EST: gi|60399456|gb|DN232268.1|DN232268
EST:     ATGATCCATCTGTTAAAGATTTGCTGGCATCGTTGCACAGCCAGGGAGAG                         CAAGAGAAGAAGGAAGACACGTCAGACAAAACAGAAGACGATAAGAACTGA
genomic: ATGATCCATCTGTTAAAGATTTGCTGGCATCGTTGCACAGCCAGGGAGAGgtatgttctt ... ttttaaacagCAAGAGAAGAAGGAAGACACGTCAGACAAAACAGAAGACGATAAGAACTGA
EST: gi|37383796|gb|CF628931.1|CF628931
EST:     ATGATCCATCTGTTAAAGATTTGCTGGCATCGTTGCACAGCCAGGGAGAG                         CAAGAGAAGAAGGAAGACACGTCAGACAAAACAGAAGACGATAAGAACTGA
genomic: ATGATCCATCTGTTAAAGATTTGCTGGCATCGTTGCACAGCCAGGGAGAGgtatgttctt ... ttttaaacagCAAGAGAAGAAGGAAGACACGTCAGACAAAACAGAAGACGATAAGAACTGA
EST: gi|32930239|gb|CF035051.1|CF035051
EST:     ATGATCCATCTGTTAAAGATTTGCTGGCATCGTTGCACAGCCAGGGAGAG                         CAAGAGAAGAAGGAAGACACGTCAGACAAAACAGAAGACGAGAAGAACTGA
genomic: ATGATCCATCTGTTAAAGATTTGCTGGCATCGTTGCACAGCCAGGGAGAGgtatgttctt ... ttttaaacagCAAGAGAAGAAGGAAGACACGTCAGACAAAACAGAAGACGATAAGAACTGA

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: 261

CTTCCTGGTGTTGATCCCAATGATCCATCTGTTAAAGATTTGCTGGCATCGTTGCACAGCCAGGGAGAGgtatgttctt ... ttttaaacagCAAGAGAAGAAGGAAGACACGTCAGACAAAACAGAAGACGATAAGAACTGATATAGCCATGTTCACGCTTCCAT


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 211

CTTCCTGGTGTTGATCCCAATGATCCATCTGTTAAAGATTTGCTGGCATCGTTGCACAGCCAGGGAGAGgtatgttctt ... ttttaaacagCAAGAGAAGAAGGAAGACACGTCAGACAAAACAGAAGACGATAAGAACTGATATAGCCATGTTCACGCTTCCAT


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 120

CTTCCTGGTGTTGATCCCAATGATCCATCTGTTAAAGATTTGCTGGCATCGTTGCACAGCCAGGGAGAGgtatgttctt ... ttttaaacagCAAGAGAAGAAGGAAGACACGTCAGACAAAACAGAAGACGATAAGAACTGATATAGCCATGTTCACGCTTCCAT


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 306

CTTCCTGGTGTTGATCCCAATGATCCATCTGTTAAAGATTTGCTGGCATCGTTGCACAGCCAGGGAGAGgtatgttctt ... ttttaaacagCAAGAGAAGAAGGAAGACACGTCAGACAAAACAGAAGACGATAAGAACTGATATAGCCATGTTCACGCTTCCAT