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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...atgcaaggcagagctctttaaaaaaagttctaatgtgatgtgccctgatgaggcaacggtggcaacgctgcaagatttcttatactcttttgttttacagTTTCACGTAAACTGCATCGACCCATGGCTGCGCCAACAGGGTACATGCCCAATCTGCAAGCACCAGGTGAGCGATGGGTGGCATGCTACAGGCAACGGTG

Basic information

species Zea mays
transcript GRMZM2G337425_T03
intron # 7
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G337425_T03 (Zea mays), 3'ss of exon 7
lower sequence: LOC_Os03g16570.3 (Oryza sativa), 3'ss of exon 8
atgcaaggcagagctctttaaaaaaagttcta-at--gtgatgtgccctgatgaggcaacggtggcaacgctgcaagattt-cttatactctt--ttgttttacagTTTCACGTAAACTGCATCGACCCATGGCTGCGCCAACAGGGTACATGCCCAATCTGCAAGCACCAGGTGAGCGATGGGTGGCATGCTACAGGCAACGGTG
           |||| |  |   || | |  | ||  ||| | |    |  |   |  | |  ||     ||||||| ||| ||||   ||    ||||||| |||||||| | |||||||||||| |||||| ||||||||||||| ||||||||| | ||||||||||  || |||||||||||||||| |  ||   | | | 
-----gtttttagctttccatcgaaggattgacattggtgctattagttttttgtgtcatga-ggtgggactgcaaggtttacttactttcccacttgttttgcagTTTCATGCAAACTGCATCGATCCATGGTTGCGCCAACAGGGAACATGCCCAGTTTGCAAGCACCGTGTAAGCGATGGGTGGCATGGTGAAGCAGATGCTT

upper sequence: GRMZM2G337425_T03 (Zea mays), 3'ss of exon 7
lower sequence: GLYMA11G34130.2 (Glycine max), 3'ss of exon 8
--atgcaaggcaga-gctctttaaaaaaagttctaatgtgatgtgccctgatgaggcaacggtggcaacgctgcaagatttcttatactcttttgttttacagTTTCACGTAAACTGCATCGACCCATGGCTGCGCCAACAGGGTACATGCCCAATCTGCAAGCACCAGGTGAGCGATGGGTGGCATGCTACAGGCAACGGTG
  | | | | | || | ||  |||||  |||  | || |  |||       |    |     ||| |   |||  |  ||  ||||  | || | ||||  |||||||||  ||||||||||| || |||||||||||||| || ||||||||  | || ||    |  |   |   ||| |||  ||  |  ||  |   ||
acaagtatgtctgaagttcaataaaatcagtgttgatattctgtatttatttatctcgtgaatggta---ctgacaccttgtttatgtttttattttttgaagTTTCACGCTAACTGCATCGATCCCTGGCTGCGCCAACAAGGGACATGCCCTGTATGTAAATTTCGAGCTGGATCTGGTTGGAGTGACAATGGACATAATG

upper sequence: GRMZM2G337425_T03 (Zea mays), 3'ss of exon 7
lower sequence: GLYMA18G04160.1 (Glycine max), 3'ss of exon 9
--atgcaaggcagagctctttaaaaaaagttctaatgtgatgtgccctgatgaggcaacggtggcaacgctgcaagatttcttatactcttttgttttacagTTTCACGTAAACTGCATCGACCCATGGCTGCGCCAACAGGGTACATGCCCAATCTGCAAGCACCAGGTGAGCGATGGGTGGCATGCTACAGGCAACGGTG
  |||      | || ||  |||||  | |  | || |  ||     |  | |    | |          ||  |  ||  ||||  | || | ||||  ||||||||| ||| |||||||| || |||||||||||||| || ||||||||  | || ||    |  |   |   ||| |||  ||  |  ||  |   | 
acatgatgtctaaagttcaataaaatcattgttgatattctgcatt-tatttatctcatgtgaatggtattgacaccttgtttatgtttttattttttgaaGTTTCACGCAAATTGCATCGATCCCTGGCTGCGCCAACAAGGGACATGCCCTGTATGTAAATTTCGAGCTGGATCTGGTTGGAGTGACAATGGACATAAT-

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|18166650|gb|BM336489.1|BM336489
EST:     AGCAAGTCACGGTTGGTGATCTGTTGAGAAGCCTACCATGCTTGCATCAG                         TTTCACGTAAACTGCATCGACCCATG
genomic: AGCAAGTCACGGTGGGTGATCTGTTGAGAAGCCTACCATGCTTGCATCAGgtaatcatac ... tgttttacagTTTCACGTAAACTGCATCGACCCATG
EST: gi|1298525|gb|W21775.1|W21775
EST:     AGCAAGTCACGGTGGGTGATATGTTGAGAAGCCTACCATGCTTGCATCAG                         TTTCACGTAAACTGCATCGACCCATGGCTGCG-CAACAGGGTACATGCCCA
genomic: AGCAAGTCACGGTGGGTGATCTGTTGAGAAGCCTACCATGCTTGCATCAGgtaatcatac ... tgttttacagTTTCACGTAAACTGCATCGACCCATGGCTGCGCCAACAGGGTACATGCCCA
EST: gi|148928861|gb|EC873779.2|EC873779
EST:     AGCAAGTCACGGTGGGTGATCTGTTGAGAAGCCTACCATGCTTGCATCAG                         TTTCACGTAAACTGCATCGACCCATGGCTGCGCCAACAGGGTACATGCCCA
genomic: AGCAAGTCACGGTGGGTGATCTGTTGAGAAGCCTACCATGCTTGCATCAGgtaatcatac ... tgttttacagTTTCACGTAAACTGCATCGACCCATGGCTGCGCCAACAGGGTACATGCCCA
EST: gi|18164717|gb|BM334556.1|BM334556
EST:     AGCAAGTCACGGTGGGTGATCTGTTGAGAAGCCTACCATGCTTGCATCAG                         TTTCACGTAAACTGCATCGACCCATGGCTGCGCCAACAGGGTACATGCCCA
genomic: AGCAAGTCACGGTGGGTGATCTGTTGAGAAGCCTACCATGCTTGCATCAGgtaatcatac ... tgttttacagTTTCACGTAAACTGCATCGACCCATGGCTGCGCCAACAGGGTACATGCCCA
EST: gi|91056515|gb|EB166933.1|EB166933
EST:     AGCAAGTCACGGTGGGTGATCTGTTGAGAAGCCTACCATGCTTGCATCAG                         TTTCACGTAAACTGCATCGACCCATGGCTGCGCCAACAGGGTACATGCCCA
genomic: AGCAAGTCACGGTGGGTGATCTGTTGAGAAGCCTACCATGCTTGCATCAGgtaatcatac ... tgttttacagTTTCACGTAAACTGCATCGACCCATGGCTGCGCCAACAGGGTACATGCCCA
EST: gi|86467591|gb|DY233961.1|DY233961
EST:     AGCAAGTCACGGTGGGTGATCTGTTGAGAAGCCTACCATGCTTGCATCAG                         TTTCACGTAAACTGCATCGACCCATGGCTGCGCCAACAGGGTACATGCCCA
genomic: AGCAAGTCACGGTGGGTGATCTGTTGAGAAGCCTACCATGCTTGCATCAGgtaatcatac ... tgttttacagTTTCACGTAAACTGCATCGACCCATGGCTGCGCCAACAGGGTACATGCCCA
EST: gi|71760470|gb|DR958407.1|DR958407
EST:     AGCAAGTCACGGTGGGTGATCTGTTGAGAAGCCTACCATGCTTGCATCAG                         TTTCACGTAAACTGCATCGACCCATGGCTGCGCCAACAGGGTACATGCCCA
genomic: AGCAAGTCACGGTGGGTGATCTGTTGAGAAGCCTACCATGCTTGCATCAGgtaatcatac ... tgttttacagTTTCACGTAAACTGCATCGACCCATGGCTGCGCCAACAGGGTACATGCCCA
EST: gi|78083978|gb|DV512371.1|DV512371
EST:     AGCAAGTCACGGTGGGTGATCTGTTGAGAAGCCTACCATGCTTGCATCAG                         TTTCACGTAAACTGCATCGACCCATGGCTGCGCCAACAGGGTACATGCCCA
genomic: AGCAAGTCACGGTGGGTGATCTGTTGAGAAGCCTACCATGCTTGCATCAGgtaatcatac ... tgttttacagTTTCACGTAAACTGCATCGACCCATGGCTGCGCCAACAGGGTACATGCCCA
EST: gi|78085072|gb|DV513465.1|DV513465
EST:     AGCAAGTCACGGTGGGTGATCTGTTGAGAAGCCTACCATGCTTGCATCAG                         TTTCACGTAAACTGCATCGACCCATGGCTGCGCCAACAGGGTACATGCCCA
genomic: AGCAAGTCACGGTGGGTGATCTGTTGAGAAGCCTACCATGCTTGCATCAGgtaatcatac ... tgttttacagTTTCACGTAAACTGCATCGACCCATGGCTGCGCCAACAGGGTACATGCCCA
EST: gi|76288197|gb|DV027765.1|DV027765
EST:     AGCAAGTCACGGTGGGTGATCTGTTGAGAAGCCTACCATGCTTGCATCAG                         TTTCACGTAAACTGCATCGACCCATGGCTGCGCCAACAGGGTACATGCCCA
genomic: AGCAAGTCACGGTGGGTGATCTGTTGAGAAGCCTACCATGCTTGCATCAGgtaatcatac ... tgttttacagTTTCACGTAAACTGCATCGACCCATGGCTGCGCCAACAGGGTACATGCCCA
EST: gi|86467324|gb|DY233694.1|DY233694
EST:     AGCAAGTCACGGTGGGTGATTTGTTGAGAAGCCTACCATGCTTGCATCAG                         TTTCACGTAAACTGCATCGACCCATGGCTGCGCCAACAGGGTACATGCCCA
genomic: AGCAAGTCACGGTGGGTGATCTGTTGAGAAGCCTACCATGCTTGCATCAGgtaatcatac ... tgttttacagTTTCACGTAAACTGCATCGACCCATGGCTGCGCCAACAGGGTACATGCCCA

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), 47 (downstream exon)
Score: 141

TGGAACCAGCAAACCTTCAGAGGATGAACTAACATGTAGTGTTTGCTTAGAGCAAGTCACGGTGGGTGATCTGTTGAGAAGCCTACCATGCTTGCATCAGgtaatcatac ... tgttttacagTTTCACGTAAACTGCATCGACCCATGGCTGCGCCAACAGGGTACATGCCCAATCTGCAAGCACCAGGTGAGCGATGGGTGGCATGCTACAGGCAACGGTG


Block sizes: 45 (upstream exon), 49 (downstream exon)
Score: 28

TGGAACCAGCAAACCTTCAGAGGATGAACTAACATGTAGTGTTTGCTTAGAGCAAGTCACGGTGGGTGATCTGTTGAGAAGCCTACCATGCTTGCATCAGgtaatcatac ... tgttttacagTTTCACGTAAACTGCATCGACCCATGGCTGCGCCAACAGGGTACATGCCCAATCTGCAAGCACCAGGTGAGCGATGGGTGGCATGCTACAGGCAACGGTG


Block sizes: 38 (upstream exon), 49 (downstream exon)
Score: 50

TGGAACCAGCAAACCTTCAGAGGATGAACTAACATGTAGTGTTTGCTTAGAGCAAGTCACGGTGGGTGATCTGTTGAGAAGCCTACCATGCTTGCATCAGgtaatcatac ... tgttttacagTTTCACGTAAACTGCATCGACCCATGGCTGCGCCAACAGGGTACATGCCCAATCTGCAAGCACCAGGTGAGCGATGGGTGGCATGCTACAGGCAACGGTG


Block sizes: 44 (upstream exon), 48 (downstream exon)
Score: 57

TGGAACCAGCAAACCTTCAGAGGATGAACTAACATGTAGTGTTTGCTTAGAGCAAGTCACGGTGGGTGATCTGTTGAGAAGCCTACCATGCTTGCATCAGgtaatcatac ... tgttttacagTTTCACGTAAACTGCATCGACCCATGGCTGCGCCAACAGGGTACATGCCCAATCTGCAAGCACCAGGTGAGCGATGGGTGGCATGCTACAGGCAACGGTG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgatgaggcaacggtggcaacgctgcaagatttcttatactcttttgttttacagTTTCACGTAAACTGCATCGACCCATGGCTGCGCCAACAGGGTACATGCCCAATCTGCAAGCACCAGGTGAGCGATGGGTGGCATGCTACAGGCAACGGTG
 ccctgat  putative branch site (score: 57)
                              tttcttatactctttt  putative PPT
                             atttcttata  TA-rich tract