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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaatgctttgttgaatgtcttttattttctcctcagctactgcagatagattggcggctaatcttttcacaatctttagCGGTGAGCCCCTGACTGTCCAGAGGCCAGGAACACAGACTAGGAGTTTCTGCTATGTTGCCGATATG

Basic information

species Zea mays
transcript GRMZM2G165357_T01
intron # 9
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G165357_T02 (Zea mays), 3'ss of exon 8
lower sequence: LOC_Os03g16980.4 (Oryza sativa), 3'ss of exon 9
gtaatgctttgttgaatgtcttttattttctcctcagctactg--cagatagattggcggctaatctt--ttcacaatctt-tagCGGTGAGCCCCTGACTGTCCAGAGGCCAGGAACACAGACTAGGAGTTTCTGCTATGTTGCCGATATG---------------------------------
||||||||  | ||||  ||||| |   |   ||||| |  ||  ||| | |    |  ||| || ||  | || ||| ||  || || |||||||||||||| |||| |||||||||||| |||||||| |||||||||||||| || |||                                 
gtaatgctc-gctgaacttctttcaacattctctcaggttgtgtccagttggtcctggagcttattttcatacataattttacagTGGCGAGCCCCTGACTGTTCAGAAGCCAGGAACACAAACTAGGAGCTTCTGCTATGTTGCTGACATGGTTTGTCACCCCTTTTGAAATGTCATTAATTAA

upper sequence: GRMZM2G165357_T02 (Zea mays), 3'ss of exon 8
lower sequence: LOC_Os03g16980.3 (Oryza sativa), 3'ss of exon 8
gtaatgctttgttgaatgtcttttattttctcctcagctactg--cagatagattggcggctaatctt--ttcacaatctt-tagCGGTGAGCCCCTGACTGTCCAGAGGCCAGGAACACAGACTAGGAGTTTCTGCTATGTTGCCGATATG
||||||||  | ||||  ||||| |   |   ||||| |  ||  ||| | |    |  ||| || ||  | || ||| ||  || || |||||||||||||| |||| |||||||||||| |||||||| |||||||||||||| || |||
gtaatgctc-gctgaacttctttcaacattctctcaggttgtgtccagttggtcctggagcttattttcatacataattttacagTGGCGAGCCCCTGACTGTTCAGAAGCCAGGAACACAAACTAGGAGCTTCTGCTATGTTGCTGACATG
















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|18169307|gb|BM339147.1|BM339147
EST:     CGTGTTGTTAGCAACTTCATTGCTCAGGCTGTGCG                         CGGTGAGCCCCTGACTGTCCAGAGGCCAGGAACACAGACTAGGAGTTTCTG
genomic: CGTGTTGTTAGCAACTTCATTGCTCAGGCTGTGCGgtaatgcttt ... caatctttagCGGTGAGCCCCTGACTGTCCAGAGGCCAGGAACACAGACTAGGAGTTTCTG
EST: gi|13562266|gb|BG550486.1|BG550486
EST:     ACATTGATGATGGCCGTGTTGCTAGCAACTTCATCTGCTCAGGCTGTGCG                         CGGTGAGCCCCTGACTGTCCAGAGGCCAGGAACACAGACTAGGAGTTTTCT
genomic: ACATTGATGATGGCCGTGTTGTTAGCAACTTCAT-TGCTCAGGCTGTGCGgtaatgcttt ... caatctttagCGGTGAGCCCCTGACTGTCCAGAGGCCAGGAACACAGACTAGGAG-TTTCT
EST: gi|13558126|gb|BG549482.1|BG549482
EST:     AACATTGATGATGGCCGTGTTGTTAGCAACTTCATTGCTCAGGCTGTGCG                         CGGTGAGCCCCTGACTGTCCAGAGGCCAGGAACACTGTATTAGGAGTTTCT
genomic: AACATTGATGATGGCCGTGTTGTTAGCAACTTCATTGCTCAGGCTGTGCGgtaatgcttt ... caatctttagCGGTGAGCCCCTGACTGTCCAGAGGCCAGGAACACAG-ACTAGGAGTTTCT
EST: gi|32850602|gb|CD990283.1|CD990283
EST:     AACATTGATGATGGCCGTGTTGTTAGCAACTTCATTGCTCAGGCTGTGCG                         CGGCGAGCCCCTGACTGTCCAGAGGCTAGGAACACAGACTAGGAGTTTTTG
genomic: AACATTGATGATGGCCGTGTTGTTAGCAACTTCATTGCTCAGGCTGTGCGgtaatgcttt ... caatctttagCGGTGAGCCCCTGACTGTCCAGAGGCCAGGAACACAGACTAGGAGTTTCTG
EST: gi|18172685|gb|BM348073.1|BM348073
EST:     AACATTGATGATGGCCGTGTTGTTAGCAACTTCATTGCTCAGGCTGTGCG                         CGGTGAGCCCCTGACTGTCCAGAGGCCAGGAACACAGACTAGGAGTTTCTG
genomic: AACATTGATGATGGCCGTGTTGTTAGCAACTTCATTGCTCAGGCTGTGCGgtaatgcttt ... caatctttagCGGTGAGCCCCTGACTGTCCAGAGGCCAGGAACACAGACTAGGAGTTTCTG
EST: gi|149070502|gb|EE158906.2|EE158906
EST:     AACATTGATGATGGCCGTGTTGTTAGCAACTTCATTGCTCAGGCTGTGCG                         CGGTGAGCCCCTGACTGTCCAGAGGCCAGGAACACAGACTAGGAGTTTCTG
genomic: AACATTGATGATGGCCGTGTTGTTAGCAACTTCATTGCTCAGGCTGTGCGgtaatgcttt ... caatctttagCGGTGAGCCCCTGACTGTCCAGAGGCCAGGAACACAGACTAGGAGTTTCTG
EST: gi|71444249|gb|DR825299.1|DR825299
EST:     AACTTCATTGCTCAGGCTGTGCG                         CGGTGAGCCCCTGACTGTCCAGAGGCCAGGAACACAGACTAGGAGTTTCTG
genomic: AACTTCATTGCTCAGGCTGTGCGgtaatgcttt ... caatctttagCGGTGAGCCCCTGACTGTCCAGAGGCCAGGAACACAGACTAGGAGTTTCTG
EST: gi|60394382|gb|DN227252.1|DN227252
EST:     AACATTGATGATGGCCGTGTTGTTAGCAACTTCATTGCTCAGGCTGTGCG                         CGGTGAGCCCCTGACTGTCCAGAGGCCAGGAACACAGACTAGGAGTTTCTG
genomic: AACATTGATGATGGCCGTGTTGTTAGCAACTTCATTGCTCAGGCTGTGCGgtaatgcttt ... caatctttagCGGTGAGCCCCTGACTGTCCAGAGGCCAGGAACACAGACTAGGAGTTTCTG
EST: gi|6012581|gb|AW062018.1|AW062018
EST:     CTTCATTGCTCAGGCTGTGCG                         CGGTGAGCCCCTGACTGTCCAGAGGCCAGGAACCCAGACTAGGAGTTTCTG
genomic: CTTCATTGCTCAGGCTGTGCGgtaatgcttt ... caatctttagCGGTGAGCCCCTGACTGTCCAGAGGCCAGGAACACAGACTAGGAGTTTCTG
EST: gi|71444250|gb|DR825300.1|DR825300
EST:     AACATTGATGATGGGCGTGTTGTTAGCAACTTCATTGCTCAGGCTGTGCG                         CGGTGAGCCCCTGA
genomic: AACATTGATGATGGCCGTGTTGTTAGCAACTTCATTGCTCAGGCTGTGCGgtaatgcttt ... caatctttagCGGTGAGCCCCTGA
EST: gi|149082965|gb|EE172201.2|EE172201
EST:     AACATTGATGATGGCCGTGTTGTTAGCAACTTCATTGCTCAGGCTGTGCG                         CGGTGAGCCCCTGACTGTCCAGAGGCCAGGAACACAGACTAGGAGTTTCTG
genomic: AACATTGATGATGGCCGTGTTGTTAGCAACTTCATTGCTCAGGCTGTGCGgtaatgcttt ... caatctttagCGGTGAGCCCCTGACTGTCCAGAGGCCAGGAACACAGACTAGGAGTTTCTG
EST: gi|71449953|gb|DR831003.1|DR831003
EST:     AACATTGATGATGGCCGTGTTGTTAGCAACTTCATTGCTCANGCTGTGCG                         CGGTGAGCCCCTGACTG
genomic: AACATTGATGATGGCCGTGTTGTTAGCAACTTCATTGCTCAGGCTGTGCGgtaatgcttt ... caatctttagCGGTGAGCCCCTGACTG
EST: gi|60342197|gb|DN209170.1|DN209170
EST:     CATTGATGATGGCCCGTGTTGTTAGCAACTTTCATTGCTCAGGCTGTGCG                         CGGTGAGCCCCTGACTGTCCAGAGGCCAGGAACACAGACTAGGAGTTTCTG
genomic: CATTGATGATGG-CCGTGTTGTTAGCAAC-TTCATTGCTCAGGCTGTGCGgtaatgcttt ... caatctttagCGGTGAGCCCCTGACTGTCCAGAGGCCAGGAACACAGACTAGGAGTTTCTG
EST: gi|71449952|gb|DR831002.1|DR831002
EST:     AACATTGATGATGGCCGTGTTGTTAGCAACTTCATTGCTCAGGCTGTGCG                         CGGTGAGCCCCTGACTGTCCAGAGGCCAGGAACACAGACTAGGAGTTTCTG
genomic: AACATTGATGATGGCCGTGTTGTTAGCAACTTCATTGCTCAGGCTGTGCGgtaatgcttt ... caatctttagCGGTGAGCCCCTGACTGTCCAGAGGCCAGGAACACAGACTAGGAGTTTCTG
EST: gi|149082964|gb|EE172200.2|EE172200
EST:     GCCGTGTTGTTAGCAACTTCATTGCTCAGGCTGTGCG                         CGGTGAGCCCCTGACTGTCCAGAGGCCAGGAACACAGACTAGGAGTTTCTG
genomic: GCCGTGTTGTTAGCAACTTCATTGCTCAGGCTGTGCGgtaatgcttt ... caatctttagCGGTGAGCCCCTGACTGTCCAGAGGCCAGGAACACAGACTAGGAGTTTCTG
EST: gi|18171739|gb|BM341579.1|BM341579
EST:     GATGATGNCCGTGTTGTTAGCAACTTCATTGCTCAGGCTGTGCG                         CGGTGAGCCCCTGACTGTCCAGAGGCCAGGAACACAGACTAGGAGTTTCTG
genomic: GATGATGGCCGTGTTGTTAGCAACTTCATTGCTCAGGCTGTGCGgtaatgcttt ... caatctttagCGGTGAGCCCCTGACTGTCCAGAGGCCAGGAACACAGACTAGGAGTTTCTG
EST: gi|149070980|gb|EE159385.2|EE159385
EST:     AACATTGATGATGGCCGTGTTGTTAGCAACTTCATTGCTCAGGCTGTGCG                         CGGTGAGCCCCTGACTGTC
genomic: AACATTGATGATGGCCGTGTTGTTAGCAACTTCATTGCTCAGGCTGTGCGgtaatgcttt ... caatctttagCGGTGAGCCCCTGACTGTC
EST: gi|149065531|gb|EE286651.2|EE286651
EST:     AACATTGATGATGGCCGTGTTGTTAGCAACTTCATTGCTCAGGCTGTGCG                         CGGTGAGCCCCTGACTGTCCAGAGGCCAGGAACACAGACTAGGAGTTTCTG
genomic: AACATTGATGATGGCCGTGTTGTTAGCAACTTCATTGCTCAGGCTGTGCGgtaatgcttt ... caatctttagCGGTGAGCCCCTGACTGTCCAGAGGCCAGGAACACAGACTAGGAGTTTCTG
EST: gi|60339871|gb|DN206844.1|DN206844
EST:     AACATTGATGATGGCCGTGTTGTTAGCAACTTCATTGCTCAGGCTGTGCG                         CGGTGAGCCCCTGACTGTCCAGAGGCCAGGAACACAGACTAGGAGTTTCTG
genomic: AACATTGATGATGGCCGTGTTGTTAGCAACTTCATTGCTCAGGCTGTGCGgtaatgcttt ... caatctttagCGGTGAGCCCCTGACTGTCCAGAGGCCAGGAACACAGACTAGGAGTTTCTG
EST: gi|18173577|gb|BM348965.1|BM348965
EST:     AACATTGATGATGGCCGTGTTGTTAGCAACTTCATTGCTCAGGCTGTGCG                         CGGTGAGCCCCTGACTGTCCAGAGGCCAGGAACACAGACTAGGAGTTTCTG
genomic: AACATTGATGATGGCCGTGTTGTTAGCAACTTCATTGCTCAGGCTGTGCGgtaatgcttt ... caatctttagCGGTGAGCCCCTGACTGTCCAGAGGCCAGGAACACAGACTAGGAGTTTCTG
EST: gi|18176777|gb|BM351710.1|BM351710
EST:     AACATTGATGATGGCCGTGTTGTTAGCAACTTCATTGCTCAGGCTGTGCG                         CGGTGAGCCCCTGACTGTCCAGAGGCCAGGAACACAGACTAGGAGTTTCTG
genomic: AACATTGATGATGGCCGTGTTGTTAGCAACTTCATTGCTCAGGCTGTGCGgtaatgcttt ... caatctttagCGGTGAGCCCCTGACTGTCCAGAGGCCAGGAACACAGACTAGGAGTTTCTG
EST: gi|149070503|gb|EE158907.2|EE158907
EST:     AACATTGATGATGGCCGTGTTGTTAGCAACTTCATTGCTCANGCTGTGCG                         CGGTGAGCCCCTGACTG
genomic: AACATTGATGATGGCCGTGTTGTTAGCAACTTCATTGCTCAGGCTGTGCGgtaatgcttt ... caatctttagCGGTGAGCCCCTGACTG
EST: gi|45213764|gb|CK850000.1|CK850000
EST:     AACATTGATGATGGCCGTGTTGTTAGCAACTTCATTGCTCAGGCTGTGCG                         CGGTGAGCCCCTGACTGTCCAGAGGCCAGGAACACAGACTAGGAGTTTTTG
genomic: AACATTGATGATGGCCGTGTTGTTAGCAACTTCATTGCTCAGGCTGTGCGgtaatgcttt ... caatctttagCGGTGAGCCCCTGACTGTCCAGAGGCCAGGAACACAGACTAGGAGTTTCTG

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: 158

AAATCCGGATTGCCAGGATTTTCAACACCTATGGGCCTAGGATGAACATTGATGATGGCCGTGTTGTTAGCAACTTCATTGCTCAGGCTGTGCGgtaatgcttt ... caatctttagCGGTGAGCCCCTGACTGTCCAGAGGCCAGGAACACAGACTAGGAGTTTCTGCTATGTTGCCGATATG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 377

AAATCCGGATTGCCAGGATTTTCAACACCTATGGGCCTAGGATGAACATTGATGATGGCCGTGTTGTTAGCAACTTCATTGCTCAGGCTGTGCGgtaatgcttt ... caatctttagCGGTGAGCCCCTGACTGTCCAGAGGCCAGGAACACAGACTAGGAGTTTCTGCTATGTTGCCGATATG


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 396

AAATCCGGATTGCCAGGATTTTCAACACCTATGGGCCTAGGATGAACATTGATGATGGCCGTGTTGTTAGCAACTTCATTGCTCAGGCTGTGCGgtaatgcttt ... caatctttagCGGTGAGCCCCTGACTGTCCAGAGGCCAGGAACACAGACTAGGAGTTTCTGCTATGTTGCCGATATG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 733

AAATCCGGATTGCCAGGATTTTCAACACCTATGGGCCTAGGATGAACATTGATGATGGCCGTGTTGTTAGCAACTTCATTGCTCAGGCTGTGCGgtaatgcttt ... caatctttagCGGTGAGCCCCTGACTGTCCAGAGGCCAGGAACACAGACTAGGAGTTTCTGCTATGTTGCCGATATG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttttctcctcagctactgcagatagattggcggctaatcttttcacaatctttagCGGTGAGCCCCTGACTGTCCAGAGGCCAGGAACACAGACTAGGAGTTTCTGCTATGTTGCCGATATG
                               ggctaat  putative branch site (score: 733)
                                     tcttttcac  CT-rich tract
                                  taatctttt  TA-rich tract