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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaactgttactccaacttgtggcgatgaatatgttttaatttgcatatgtgaagggaaaaagagatgtgaccatgattgggtgtatgacagGCTGAGCTGATGTACGAGACAATCCGCGAATGGCCAAGATATGTCAATGTCCCTCTTCCTGTTGCAAGG

Basic information

species Zea mays
transcript GRMZM2G143651_T01
intron # 9
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G143651_T01 (Zea mays), 3'ss of exon 9
lower sequence: LOC_Os02g57180.2 (Oryza sativa), 3'ss of exon 7
gtaactgttactc-caacttgtggcgatgaat--atgttttaatttgcatatgtgaagggaaaaagag---atgtgaccatgattgggtgtatgacagGCTGAGCTGATGTACGAGACAATCCGCGAATGGCCAAGATATGTCAATGTCCCTCTTCCTGTTGCAAGG
|||| | | |  | |||| | | |  ||| |   |||    ||| | ||  |  |  ||   |        || | |  ||| |  ||  | | |||||||||||||||||| |||||||| || ||||||||| | ||  || |||| ||||||||| ||||||||
gtaattatcatgcacaacattttgttatgcagcaatgaacgaatcttcaagttggttggtcgagtttttttatataaaaatgttctgg-atgttacagGCTGAGCTGATGTATGAGACAATACGTGAATGGCCACGGTACATCGATGTTCCTCTTCCTATTGCAAGG
















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|32926106|gb|CF030918.1|CF030918
EST:     GAAAGATATATGAACTTGGGGGGCCTGAAATTTACACTGTCCATGAGCTG                         GCTGAGCTGATGTAC
genomic: GAAAGATATATGAACTTGGGGGCCCTGAAATTTACACTGTCCATGAGCTGgtaactgtta ... tgtatgacagGCTGAGCTGATGTAC
EST: gi|32926653|gb|CF031465.1|CF031465
EST:     GAAAGATATATGAACTTGGGGGGCCTGAAATTTACACTGTCCATGAGCTG                         GCTGAGCTGATGT
genomic: GAAAGATATATGAACTTGGGGGCCCTGAAATTTACACTGTCCATGAGCTGgtaactgtta ... tgtatgacagGCTGAGCTGATGT
EST: gi|7216537|gb|AW562659.1|AW562659
EST:     GAAAGATATATGAACTTGGGGGCCCTGAAATTTACACTGTCCATGAGCTG                         GCTGAGCTGATGTACGAGACAATCCGCGAATGGGCAAGATATGGCAATG
genomic: GAAAGATATATGAACTTGGGGGCCCTGAAATTTACACTGTCCATGAGCTGgtaactgtta ... tgtatgacagGCTGAGCTGATGTACGAGACAATCCGCGAATGGCCAAGATATGTCAATG
EST: gi|71533831|gb|DR784590.1|DR784590
EST:     GAAAGATATATGAACTTGGGGGCCCTGAAATTTACACTGTCCATGAGCTG                         GCTGAGCTGATGTACGAGACAATCCGCGAATGGCCAAGATATGTCGATGTC
genomic: GAAAGATATATGAACTTGGGGGCCCTGAAATTTACACTGTCCATGAGCTGgtaactgtta ... tgtatgacagGCTGAGCTGATGTACGAGACAATCCGCGAATGGCCAAGATATGTCAATGTC
EST: gi|30031664|gb|CB833515.1|CB833515
EST:     GAAAGATATATGAACTTGGGGGCCCTGAAATTTACACTGTCCATGAGCTG                         GCTGAGCTGATGTACGAGACAATCCGCGAATGGCCAAGATATGTCAATGTC
genomic: GAAAGATATATGAACTTGGGGGCCCTGAAATTTACACTGTCCATGAGCTGgtaactgtta ... tgtatgacagGCTGAGCTGATGTACGAGACAATCCGCGAATGGCCAAGATATGTCAATGTC
EST: gi|18164602|gb|BM334441.1|BM334441
EST:     GAAAGATATATGAACTTGGGGGCCCTGAAATTTACACTGTCCATGAGCTG                         GCTGAGCTGATGTACGAGACAATCCGCGAATGGCCAAGATATGTCAATGTC
genomic: GAAAGATATATGAACTTGGGGGCCCTGAAATTTACACTGTCCATGAGCTGgtaactgtta ... tgtatgacagGCTGAGCTGATGTACGAGACAATCCGCGAATGGCCAAGATATGTCAATGTC
EST: gi|32925689|gb|CF030501.1|CF030501
EST:     GAAAGATATATGAACTTGGGGGGCCTGAAATTTACACTGTCCATGAGCTG                         GCTGAGCTGATGT
genomic: GAAAGATATATGAACTTGGGGGCCCTGAAATTTACACTGTCCATGAGCTGgtaactgtta ... tgtatgacagGCTGAGCTGATGT
EST: gi|29545100|gb|CB605278.1|CB605278
EST:     CTGTCCATGAGCTG                         GCTGAGCTGATGTACGAGACAATCCGCGAATGGCCAAGATATGTCAATGTC
genomic: CTGTCCATGAGCTGgtaactgtta ... tgtatgacagGCTGAGCTGATGTACGAGACAATCCGCGAATGGCCAAGATATGTCAATGTC
EST: gi|211264901|gb|FK979901.1|FK979901
EST:     GAAAGATATATGAACTTGGGGGGCCTGAAATTTACACTGTCCATGAGCTG                         GCTGAGCTGATGTACGAGACAATCCGYGAATGGCCAAGATATGTCAATGTC
genomic: GAAAGATATATGAACTTGGGGGCCCTGAAATTTACACTGTCCATGAGCTGgtaactgtta ... tgtatgacagGCTGAGCTGATGTACGAGACAATCCGCGAATGGCCAAGATATGTCAATGTC
EST: gi|60397747|gb|DN230563.1|DN230563
EST:     GAAAGATATATGAACTTGGGGGGCCTGAAATTTACACTGTCCATGAGCTG                         GCTGAGCTGATGTACGAGACAATCCGCGAATGGCCAAGATATGTCAATGTC
genomic: GAAAGATATATGAACTTGGGGGCCCTGAAATTTACACTGTCCATGAGCTGgtaactgtta ... tgtatgacagGCTGAGCTGATGTACGAGACAATCCGCGAATGGCCAAGATATGTCAATGTC
EST: gi|67015444|gb|CO444193.1|CO444193
EST:     GAAAGATATATGAACTTGGGGGGCCTGAAATTTACACTGTCCATGAGCTG                         GCTGAGCTGATGTACGAGACAATCCGCGAATGGCCAAGATATGTCAATGTC
genomic: GAAAGATATATGAACTTGGGGGCCCTGAAATTTACACTGTCCATGAGCTGgtaactgtta ... tgtatgacagGCTGAGCTGATGTACGAGACAATCCGCGAATGGCCAAGATATGTCAATGTC
EST: gi|31350209|gb|CD434566.1|CD434566
EST:     GAAAGATATATGAACTTGGGGGGCCTGAAATTTACACTGTCCATGAGCTG                         GCTGAGCTGATGTACGAGACAATCCGCGAATGGCCAAGATATGTCAATGTC
genomic: GAAAGATATATGAACTTGGGGGCCCTGAAATTTACACTGTCCATGAGCTGgtaactgtta ... tgtatgacagGCTGAGCTGATGTACGAGACAATCCGCGAATGGCCAAGATATGTCAATGTC
EST: gi|211264900|gb|FK979900.1|FK979900
EST:     GAAAGATATATGAACTTGGGGGGCCTGAAATTTACACTGTCCATGAGCTG                         GCTGAGCTGATGTACGAGACAATCCGCGAATGGCCAAGATATGTCAATGTC
genomic: GAAAGATATATGAACTTGGGGGCCCTGAAATTTACACTGTCCATGAGCTGgtaactgtta ... tgtatgacagGCTGAGCTGATGTACGAGACAATCCGCGAATGGCCAAGATATGTCAATGTC
EST: gi|120480121|gb|EH210746.1|EH210746
EST:     GAAAGATATATGAACTTGGGGGCCCTGAAATTTACACTGTCCATGAGCTG                         GCTGAGCTGATGTACGAGACAATCCGCGAATGGCCAAGATATGTCAATGTC
genomic: GAAAGATATATGAACTTGGGGGCCCTGAAATTTACACTGTCCATGAGCTGgtaactgtta ... tgtatgacagGCTGAGCTGATGTACGAGACAATCCGCGAATGGCCAAGATATGTCAATGTC
EST: gi|32926481|gb|CF031293.1|CF031293
EST:     GAAAGATATATGAACTTGGGGGGCCTGAAATTTACACTGTCCATGAGCTG                         GCTGAGCTGATGTAC
genomic: GAAAGATATATGAACTTGGGGGCCCTGAAATTTACACTGTCCATGAGCTGgtaactgtta ... tgtatgacagGCTGAGCTGATGTAC
EST: gi|30087962|gb|CB886167.1|CB886167
EST:     GAAAGATATATGAACTTGGGGGCCCTGAAATTTACACTGTCCATGAGCTG                         GCTGAGCTGATGTACGAGACAATCCGCGAATGGCCAAGATATGTCAATGTC
genomic: GAAAGATATATGAACTTGGGGGCCCTGAAATTTACACTGTCCATGAGCTGgtaactgtta ... tgtatgacagGCTGAGCTGATGTACGAGACAATCCGCGAATGGCCAAGATATGTCAATGTC
EST: gi|71445607|gb|DR826657.1|DR826657
EST:     GAAAGATATATGAACTTGGGGGCCCTGAAATTTACACTGTCCATGAGCTG                         GCTGAGCTGATGTACGAGACAATCCGCGAATGGCCAAGATATGTCAATGTC
genomic: GAAAGATATATGAACTTGGGGGCCCTGAAATTTACACTGTCCATGAGCTGgtaactgtta ... tgtatgacagGCTGAGCTGATGTACGAGACAATCCGCGAATGGCCAAGATATGTCAATGTC
EST: gi|211383681|gb|FL229452.1|FL229452
EST:     GTCCATGAGCTG                         GCTGAGCTGATGTACGAGACAATCCGCGAATGGCCAAGATATGTCAATGTC
genomic: GTCCATGAGCTGgtaactgtta ... tgtatgacagGCTGAGCTGATGTACGAGACAATCCGCGAATGGCCAAGATATGTCAATGTC
EST: gi|32925514|gb|CF030326.1|CF030326
EST:     GAAAGATATATGAACTTGGGGGGCCTGAAATTTACACTGTCCATGAGCTG                         GCTGAGCTGATGT
genomic: GAAAGATATATGAACTTGGGGGCCCTGAAATTTACACTGTCCATGAGCTGgtaactgtta ... tgtatgacagGCTGAGCTGATGT
EST: gi|31612342|gb|CD568964.1|CD568964
EST:     GAAAGATATATGAACTTGGGGGCCCTGAAATTTACACTGTCCATGAGCTG                         GCTGAGCTGATGTACGAGACAATCCGCGAATGGCCAAGATATGTCAATGTC
genomic: GAAAGATATATGAACTTGGGGGCCCTGAAATTTACACTGTCCATGAGCTGgtaactgtta ... tgtatgacagGCTGAGCTGATGTACGAGACAATCCGCGAATGGCCAAGATATGTCAATGTC
EST: gi|149069993|gb|EE158393.2|EE158393
EST:     GAAAGATATATGAACTTGGGGGCCCTGAAATTTACACTGTCCATGAGCTG                         GCTGAGCTGATGTACGAGACAATCCGCGAATGGCCAAGATATGTCAATGTC
genomic: GAAAGATATATGAACTTGGGGGCCCTGAAATTTACACTGTCCATGAGCTGgtaactgtta ... tgtatgacagGCTGAGCTGATGTACGAGACAATCCGCGAATGGCCAAGATATGTCAATGTC
EST: gi|211418862|gb|FL076974.1|FL076974
EST:     ATATGAACTTGGGGGCCCTGAAATTTACACTGTCCATGAGCTG                         GCTGAGCTGATGTACGAGACAATCCGCGAATGGCCAAGATATGTCAATGTC
genomic: ATATGAACTTGGGGGCCCTGAAATTTACACTGTCCATGAGCTGgtaactgtta ... tgtatgacagGCTGAGCTGATGTACGAGACAATCCGCGAATGGCCAAGATATGTCAATGTC
EST: gi|32926805|gb|CF031617.1|CF031617
EST:     GAAAGATATATGAACTTGGGGGGCCTGAAATTTACACTGTCCATGAGCTG                         GCTGAGCTGATGT
genomic: GAAAGATATATGAACTTGGGGGCCCTGAAATTTACACTGTCCATGAGCTGgtaactgtta ... tgtatgacagGCTGAGCTGATGT
EST: gi|32924876|gb|CF029688.1|CF029688
EST:     GAAAGATATATGAACTTGGGGGGCCTGAAATTTACACTGTCCATGAGCTG                         GCTGAGCTGATGT
genomic: GAAAGATATATGAACTTGGGGGCCCTGAAATTTACACTGTCCATGAGCTGgtaactgtta ... tgtatgacagGCTGAGCTGATGT
EST: gi|31664373|gb|CD573098.1|CD573098
EST:     GAAAGATATATGAACTTGGGGGCCCTGAAATTTACACTGTCCATGAGCTG                         GCTGAGCTGATGTACGAGACAATCCGCGAATGGCCAAGATATGTCAATGTC
genomic: GAAAGATATATGAACTTGGGGGCCCTGAAATTTACACTGTCCATGAGCTGgtaactgtta ... tgtatgacagGCTGAGCTGATGTACGAGACAATCCGCGAATGGCCAAGATATGTCAATGTC
EST: gi|149064146|gb|EE286442.2|EE286442
EST:     GAAAGATATATGAACTTGGGGGCCCTGAAATTTACACTGTCCATGAGCTG                         GCTGAGCTGATGTACGAGACAATCCGCGAATGGCCAAGATATGTCAATGTC
genomic: GAAAGATATATGAACTTGGGGGCCCTGAAATTTACACTGTCCATGAGCTGgtaactgtta ... tgtatgacagGCTGAGCTGATGTACGAGACAATCCGCGAATGGCCAAGATATGTCAATGTC
EST: gi|31998441|gb|CD662076.1|CD662076
EST:     GAAAGATATATGAACTTGGGGGCCCTGAAATTTACACTGTCCATGAGCTG                         GCTGAGCTGATGTACGAGACAATCCGCGAATGGCCAAGATATGTCAATGTC
genomic: GAAAGATATATGAACTTGGGGGCCCTGAAATTTACACTGTCCATGAGCTGgtaactgtta ... tgtatgacagGCTGAGCTGATGTACGAGACAATCCGCGAATGGCCAAGATATGTCAATGTC
EST: gi|32925685|gb|CF030497.1|CF030497
EST:     GAAAGATATATGAACTTGGGGGGCCTGAAATTTACACTGTCCATGAGCTG                         GTTGAGCTGATGT
genomic: GAAAGATATATGAACTTGGGGGCCCTGAAATTTACACTGTCCATGAGCTGgtaactgtta ... tgtatgacagGCTGAGCTGATGT
EST: gi|32925444|gb|CF030256.1|CF030256
EST:     GAAAGATATATGAACTTGGGGGGCCTGAAATTTACACTGTCCATGAGCTG                         GCTGAGCTGATGT
genomic: GAAAGATATATGAACTTGGGGGCCCTGAAATTTACACTGTCCATGAGCTGgtaactgtta ... tgtatgacagGCTGAGCTGATGT
EST: gi|4886142|gb|AI677262.1|AI677262
EST:     ATATATGAACTTGGGGGCCCTGAAATTTACNCTGTCCATGAGCTG                         GCTGAGCTGATGTACGAGACAATCCGCGAATGGCCAAGATATGTCAATGTC
genomic: ATATATGAACTTGGGGGCCCTGAAATTTACACTGTCCATGAGCTGgtaactgtta ... tgtatgacagGCTGAGCTGATGTACGAGACAATCCGCGAATGGCCAAGATATGTCAATGTC
EST: gi|32925655|gb|CF030467.1|CF030467
EST:     GAAAGATATATGAACTTGGGGGGCCTGAAATTTACACTGTCCATGAGCTG                         GCTGAGCTGATGT
genomic: GAAAGATATATGAACTTGGGGGCCCTGAAATTTACACTGTCCATGAGCTGgtaactgtta ... tgtatgacagGCTGAGCTGATGT

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: 638

TGTTGCTGCTGCTATTGTGAACTCCCTGAAGGATGACGGCACTAGCATGGGAAAGATATATGAACTTGGGGGCCCTGAAATTTACACTGTCCATGAGCTGgtaactgtta ... tgtatgacagGCTGAGCTGATGTACGAGACAATCCGCGAATGGCCAAGATATGTCAATGTCCCTCTTCCTGTTGCAAGG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 718

TGTTGCTGCTGCTATTGTGAACTCCCTGAAGGATGACGGCACTAGCATGGGAAAGATATATGAACTTGGGGGCCCTGAAATTTACACTGTCCATGAGCTGgtaactgtta ... tgtatgacagGCTGAGCTGATGTACGAGACAATCCGCGAATGGCCAAGATATGTCAATGTCCCTCTTCCTGTTGCAAGG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 644

TGTTGCTGCTGCTATTGTGAACTCCCTGAAGGATGACGGCACTAGCATGGGAAAGATATATGAACTTGGGGGCCCTGAAATTTACACTGTCCATGAGCTGgtaactgtta ... tgtatgacagGCTGAGCTGATGTACGAGACAATCCGCGAATGGCCAAGATATGTCAATGTCCCTCTTCCTGTTGCAAGG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 1016

TGTTGCTGCTGCTATTGTGAACTCCCTGAAGGATGACGGCACTAGCATGGGAAAGATATATGAACTTGGGGGCCCTGAAATTTACACTGTCCATGAGCTGgtaactgtta ... tgtatgacagGCTGAGCTGATGTACGAGACAATCCGCGAATGGCCAAGATATGTCAATGTCCCTCTTCCTGTTGCAAGG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

taatttgcatatgtgaagggaaaaagagatgtgaccatgattgggtgtatgacagGCTGAGCTGATGTACGAGACAATCCGCGAATGGCCAAGATATGTCAATGTCCCTCTTCCTGTTGCAAGG
 ttttaat  putative branch site (score: 1016)
                    aaaaaga  TA-rich tract