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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgagaccatacataaatgttagcaaatatcttgtgttatatttgtccagccctaacaacatcttccacagCATTTTTATGGGCTCCTTAGAAGTTCCAGCCCAGGCATCTGAAACTATTAAAGTTCCAACTGCACATTATGAATTTGGCGCCAATTTTTTAGATCCAAAG

Basic information

species Zea mays
transcript GRMZM2G174696_T01
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G174696_T01 (Zea mays), 3'ss of exon 2
lower sequence: LOC_Os03g20750.1 (Oryza sativa), 3'ss of exon 2
gtgagaccatacataaatgttagcaaatatcttgtgttatatttgtccagccctaacaacatcttccacagCATTTTTATGGGCTCCTTAGAAGTTCCAGCCCAGGCATCTGAAACTATTAAAGTTCCAACTGCACATTATGAATTTGGCGCCAATTTTTTAGATCCAAAG
|| ||   |      ||||||   |  | | |    || | || | | |    |    ||| | || ||||  |||||||||| ||||||||||||||| | ||| || |||||||||| |||||||||||  ||||||| ||||| || ||||||||| |||||||||||
gtaagggaaacagataatgttgatatgtgtttcactttcttttgggcaatttattctgacaacatcaacagTGTTTTTATGGGTTCCTTAGAAGTTCCATCTCAGTCAACTGAAACTATAAAAGTTCCAACATCACATTACGAATTCGGTGCCAATTTTATAGATCCAAAG

upper sequence: GRMZM2G174696_T01 (Zea mays), 3'ss of exon 2
lower sequence: Vv03s0097g00590.t01 (Vitis vinifera), 3'ss of exon 2
-------------------------gtgagaccatacataaatgttagcaaatatctt--gtgttatatttgtc------cagccctaacaac------------atcttcca-cagCATTTTTATGGGCTCCTTAGAAGTTCCAGCCCAGGCATCTGAAACTATTAAAGTTCCAACTGCACATTATGAATTTGGCGCCAATTTTTTAGATCCAAAG
                          |     || |  |   |||||  |  | ||||  |||||  |||| ||      ||  | | | ||             | | || | |||| | || |||||  ||   ||| ||||  | ||  | ||||||||||||||| | |||||||| |||||||| |||||||| || ||| |||| ||||||
gtagattccccctttttgtttattgttctcttcaaagtttgttgttattatttttcttttgtgttccatttttctctcatcaatcttgataatgatgccttgttaaccatctatcagCGTGTTCATGGGGCCCACTGAAATTCCTTCTCAATCCTCTGAAACTATTAAAATCCCAACTGCTCATTATGAGTTTGGCGCTAACTTTATAGACCCAAAG
















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|211089741|gb|FL262759.1|FL262759
EST:     AGATTTGACTTCACAAAAGGATTGAATCAGAAGTTTTCTCTTAGCCACAG                         CATTTTTATGGGCTCCTTAGAAGTTCCAGCCCAGGCATCTGAAACTATTAA
genomic: AGGTTTGACTTCACAAAAGGATTGAATCAGAAGTTTTCTCTTAGCCACAGgtgagaccat ... tcttccacagCATTTTTATGGGCTCCTTAGAAGTTCCAGCCCAGGCATCTGAAACTATTAA
EST: gi|51593036|gb|CV072182.1|CV072182
EST:     AGATTTGACTTCACAAAAGGATTGAATCAGAAGTTTTCTCTTAGCCACAG                         CATTTTTATGGGCTCCTTAGAAGTTCCAGCCCAGGCATCTGAAACTATTAA
genomic: AGGTTTGACTTCACAAAAGGATTGAATCAGAAGTTTTCTCTTAGCCACAGgtgagaccat ... tcttccacagCATTTTTATGGGCTCCTTAGAAGTTCCAGCCCAGGCATCTGAAACTATTAA
EST: gi|211087304|gb|FL262757.1|FL262757
EST:     AGGTTTGACTTCACAAAAGGATTGAATCAKAAGTTTTCTCT-AGC-ACAG                         CATTTTTATGGGCTCCTTAGAAGTTCCAGCCCAGGCATCTGA
genomic: AGGTTTGACTTCACAAAAGGATTGAATCAGAAGTTTTCTCTTAGCCACAGgtgagaccat ... tcttccacagCATTTTTATGGGCTCCTTAGAAGTTCCAGCCCAGGCATCTGA
EST: gi|211089744|gb|FL262762.1|FL262762
EST:     AGATTTGACTTCACAAAAGGATTGAATCAGAAGTTTTCTCTTAGCCACAG                         CATTTTTATGGGCTCCTTAGAAGTTCCAGCCCAGGCATCTGAAACTATTAA
genomic: AGGTTTGACTTCACAAAAGGATTGAATCAGAAGTTTTCTCTTAGCCACAGgtgagaccat ... tcttccacagCATTTTTATGGGCTCCTTAGAAGTTCCAGCCCAGGCATCTGAAACTATTAA
EST: gi|148937183|gb|EC881364.2|EC881364
EST:     AGGTTTGACTTCACAAAAGGATTGAATCAGAAGTTTTCTCTTAGCCACAG                         CATTTTTATGGGCTCCTTAGAAGTTCCAGCCCAGGCATCTGAAACTATTAA
genomic: AGGTTTGACTTCACAAAAGGATTGAATCAGAAGTTTTCTCTTAGCCACAGgtgagaccat ... tcttccacagCATTTTTATGGGCTCCTTAGAAGTTCCAGCCCAGGCATCTGAAACTATTAA
EST: gi|71428447|gb|DR809497.1|DR809497
EST:     AGGTTTGACTTCACAAAAGGATTGAATCAGAAGTTTTCTCTTAGCCACAG                         CATTTTTATGGGCTCCTTAGAAGTTCCAGCCCAGGCATCTGAAACTATTAA
genomic: AGGTTTGACTTCACAAAAGGATTGAATCAGAAGTTTTCTCTTAGCCACAGgtgagaccat ... tcttccacagCATTTTTATGGGCTCCTTAGAAGTTCCAGCCCAGGCATCTGAAACTATTAA
EST: gi|148944949|gb|EC890114.2|EC890114
EST:     AGGTTTGACTTCACAAAAGGATTGAATCAGAAGTTTTCTCTTAGCCACAG                         CATTTTTATGGGCTCCTTAGAAGTTCCAGCCCAGGCATCTGAAACTATTAA
genomic: AGGTTTGACTTCACAAAAGGATTGAATCAGAAGTTTTCTCTTAGCCACAGgtgagaccat ... tcttccacagCATTTTTATGGGCTCCTTAGAAGTTCCAGCCCAGGCATCTGAAACTATTAA
EST: gi|5268993|gb|AI770957.1|AI770957
EST:     AGGTTTGACTTCACAAAAGGATTGAATCAGAAGTTTTCTCTTAGCCACAG                         CATTTTTATGGGCTCCTTAGAAGTTCCAGCCCAGGCATCTGAAACTATTAA
genomic: AGGTTTGACTTCACAAAAGGATTGAATCAGAAGTTTTCTCTTAGCCACAGgtgagaccat ... tcttccacagCATTTTTATGGGCTCCTTAGAAGTTCCAGCCCAGGCATCTGAAACTATTAA
EST: gi|211402157|gb|FL346436.1|FL346436
EST:     AGGTTTGACTTCACAAAAGGATTGAATCAGAAGTTTTCTCTTAGCCACAG                         CATTTTTATGGGCTCCTTAGAAGTTCCAG
genomic: AGGTTTGACTTCACAAAAGGATTGAATCAGAAGTTTTCTCTTAGCCACAGgtgagaccat ... tcttccacagCATTTTTATGGGCTCCTTAGAAGTTCCAG
EST: gi|89762284|gb|DY689955.1|DY689955
EST:     AGGTTTGACTTCACAAAAGGATTGAATCAGAAGTTTTCTCTTAGCCACAG                         CATTTTTATGGGCTCCTTAGAAGTTCCAGCCCAGGCATCTGAAACTATTAA
genomic: AGGTTTGACTTCACAAAAGGATTGAATCAGAAGTTTTCTCTTAGCCACAGgtgagaccat ... tcttccacagCATTTTTATGGGCTCCTTAGAAGTTCCAGCCCAGGCATCTGAAACTATTAA
EST: gi|149090165|gb|EE179465.2|EE179465
EST:     AGGTTTGACTTCACAAAAGGATTGAATCAGAAGTTTTCTCTTAGCCACAG                         CATTTTTATGGGCTCCTTAGAAGTTCCAGCCCAGGCATCTGAAACTATTAA
genomic: AGGTTTGACTTCACAAAAGGATTGAATCAGAAGTTTTCTCTTAGCCACAGgtgagaccat ... tcttccacagCATTTTTATGGGCTCCTTAGAAGTTCCAGCCCAGGCATCTGAAACTATTAA
EST: gi|31353843|gb|CD438200.1|CD438200
EST:     AGATTTGTCTTCACAAAAGGATTGAATCAGAAGTTTTCTCTTAGCCACAG                         CATTTTTATGGGCTCCTTAGAAGTTCCAGCCCAGGCATCTGAAACTATTAA
genomic: AGGTTTGACTTCACAAAAGGATTGAATCAGAAGTTTTCTCTTAGCCACAGgtgagaccat ... tcttccacagCATTTTTATGGGCTCCTTAGAAGTTCCAGCCCAGGCATCTGAAACTATTAA
EST: gi|76294141|gb|DV033709.1|DV033709
EST:     AGGTTTGACTTCACAAAAGGATTGAATCAGAAGTTTTCTCTTAGCCACAG                         CATTTTTATGGGCTCCTTAGAAGTTCCAGCCCAGGCATCTGAAACTATTAA
genomic: AGGTTTGACTTCACAAAAGGATTGAATCAGAAGTTTTCTCTTAGCCACAGgtgagaccat ... tcttccacagCATTTTTATGGGCTCCTTAGAAGTTCCAGCCCAGGCATCTGAAACTATTAA

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: 45 (upstream exon), 49 (downstream exon)
Score: 99

TGTCTTTGAAGCCTGAACTTTTTGAAGGATTGAGGTTTGACTTCACAAAAGGATTGAATCAGAAGTTTTCTCTTAGCCACAGgtgagaccat ... tcttccacagCATTTTTATGGGCTCCTTAGAAGTTCCAGCCCAGGCATCTGAAACTATTAAAGTTCCAACTGCACATTATGAATTTGGCGCCAATTTTTTAGATCCAAAG


Block sizes: 45 (upstream exon), 48 (downstream exon)
Score: 62

TGTCTTTGAAGCCTGAACTTTTTGAAGGATTGAGGTTTGACTTCACAAAAGGATTGAATCAGAAGTTTTCTCTTAGCCACAGgtgagaccat ... tcttccacagCATTTTTATGGGCTCCTTAGAAGTTCCAGCCCAGGCATCTGAAACTATTAAAGTTCCAACTGCACATTATGAATTTGGCGCCAATTTTTTAGATCCAAAG


Block sizes: 44 (upstream exon), 49 (downstream exon)
Score: 71

TGTCTTTGAAGCCTGAACTTTTTGAAGGATTGAGGTTTGACTTCACAAAAGGATTGAATCAGAAGTTTTCTCTTAGCCACAGgtgagaccat ... tcttccacagCATTTTTATGGGCTCCTTAGAAGTTCCAGCCCAGGCATCTGAAACTATTAAAGTTCCAACTGCACATTATGAATTTGGCGCCAATTTTTTAGATCCAAAG


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 73

TGTCTTTGAAGCCTGAACTTTTTGAAGGATTGAGGTTTGACTTCACAAAAGGATTGAATCAGAAGTTTTCTCTTAGCCACAGgtgagaccat ... tcttccacagCATTTTTATGGGCTCCTTAGAAGTTCCAGCCCAGGCATCTGAAACTATTAAAGTTCCAACTGCACATTATGAATTTGGCGCCAATTTTTTAGATCCAAAG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atgttagcaaatatcttgtgttatatttgtccagccctaacaacatcttccacagCATTTTTATGGGCTCCTTAGAAGTTCCAGCCCAGGCATCTGAAACTATTAAAGTTCCAACTGCACATTATGAATTTGGCGCCAATTTTTTAGATCCAAAG
                                  ccctaac  putative branch site (score: 73)
                                           catcttcc  putative PPT
                  tgttatattt  TA-rich tract