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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagaaggatgtgcatagcttatggtatccctgcttatcattcctctgattgtagtttgtgacctccatgttgcgtgtctctcagGTTATGCAATTCCTTGAAGCACAAGAATACAGCATGTTTAGTCGCATTGTATTTGACACTGCCCCTACG

Basic information

species Zea mays
transcript GRMZM2G105539_T01
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G105539_T01 (Zea mays), 3'ss of exon 4
lower sequence: LOC_Os02g51100.1 (Oryza sativa), 3'ss of exon 4
gtaagaaggatgtgcatagcttatggtatccctgctt---atcattcctctgattgtagtttgtgacctccatgttgcgtgtctctcagGTTATGCAATTCCTTGAAGCACAAGAATACAGCATGTTTAGTCGCATTGTATTTGACACTGCCCCTACG
|| ||||  |   |||   | |  | | | |||| ||    |  ||  |||  || |||  ||||||  | |  |||| |      ||||||||||||||||||||||||||||| || ||||||||||| |||||||| ||||||||||| || |||
gtgagaaaaa---gcaggtcatgggctttacctggttcatcttgttgttcttcttctagcatgtgactcctac-ttgcat-----ccagGTTATGCAATTCCTTGAAGCACAAGAGTATAGCATGTTTAGACGCATTGTTTTTGACACTGCTCCAACG

upper sequence: GRMZM2G105539_T01 (Zea mays), 3'ss of exon 4
lower sequence: GLYMA20G32200.1 (Glycine max), 3'ss of exon 5
gtaagaaggatgtgca---tagcttatggtatccctgcttatcattcctctgattgta-gtttgtgacctccatg----ttgcgtgtctct---cagGTTATGCAATTCCTTGAAGCACAAGAATACAGCATGTTTAGTCGCATTGTATTTGACACTGCCCCTACG
| | | |   | || |   |   | ||  | ||  |||| || |||| | | ||  |   ||| |  | | | |     ||    | ||||   |||||||||||||| |||||| |||| ||||| |||||||||| ||| || |||||||| || || ||||||
gcaggcattttatgtactgtgattaattatttcattgctaattattcatgtaataatccattttttgctttcctaacaattaaaagcctcttgtcagGTTATGCAATTTCTTGAATCACAGGAATATAGCATGTTTACTCGAATAGTATTTGATACAGCACCTACG

upper sequence: GRMZM2G105539_T01 (Zea mays), 3'ss of exon 4
lower sequence: Vv13s0019g04590.t01 (Vitis vinifera), 3'ss of exon 5
gtaagaaggatgtgcatagctt--atggtatccctgcttatcattcctctgattgtagtttgtgacctccatgtt-----------------gcgtgtctctcagGTTATGCAATTCCTTGAAGCACAAGAATACAGCATGTTTAGTCGCATTGTATTTGACACTGCCCCTACG
          |  || | ||||   || | || ||| |  |  | | |||||||||| ||||     ||| || |                  | ||| || |||||||||||||| |||||  |||||||||| || || |||| ||| ||||| ||||| ||||| || |||
---------gttcgcctggcttttgtgatttctctggtagtattgcatctgattgtattttggattttccttgcttcctcactgatgacaaaacatgtttc-cagGTTATGCAATTTCTTGAGTCACAAGAATATAGTATATTTACTCGAATTGTTTTTGATACTGCACCCACG

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|87153613|gb|DY398402.1|DY398402
EST:     TGTTGGACACACCACCACCTGGCTTGGATGAAGCAATTGCAATTTCTAAG                         GTTATGCAATTCCTTGAAGCACAAGAATACAGCATGTTTAGTCGCATTGTA
genomic: TGTTGGACACACCACCACCTGGCTTGGATGAAGCAATTGCAATTTCTAAGgtaagaagga ... tgtctctcagGTTATGCAATTCCTTGAAGCACAAGAATACAGCATGTTTAGTCGCATTGTA
EST: gi|148958813|gb|EC905077.2|EC905077
EST:     TGTTGGACACACCACCACCTGGCTTGGATGAAGCAATTGCAATTTCTAAG                         GTTATGCAATTCCTTGAAGCACAAGAATACAGCATGTTTAGTCGCATTGTA
genomic: TGTTGGACACACCACCACCTGGCTTGGATGAAGCAATTGCAATTTCTAAGgtaagaagga ... tgtctctcagGTTATGCAATTCCTTGAAGCACAAGAATACAGCATGTTTAGTCGCATTGTA
EST: gi|5846791|gb|AI999874.1|AI999874
EST:     TGTTGGACACACCACCACCTGGCTTGGATGAAGCAATTGCAATTTCTAAG                         GTTATGCAATTCCTTGAAGCACAAGAATACAGCATGTTTAGTCGCATTGTA
genomic: TGTTGGACACACCACCACCTGGCTTGGATGAAGCAATTGCAATTTCTAAGgtaagaagga ... tgtctctcagGTTATGCAATTCCTTGAAGCACAAGAATACAGCATGTTTAGTCGCATTGTA
EST: gi|6973389|gb|AW438083.1|AW438083
EST:     TGGATGAAGCAATTGCAATTTCTAAG                         GCTATGCAATTCCTTGAAGCACAAGAATACAGCATGTTTAGTCGCATTGTA
genomic: TGGATGAAGCAATTGCAATTTCTAAGgtaagaagga ... tgtctctcagGTTATGCAATTCCTTGAAGCACAAGAATACAGCATGTTTAGTCGCATTGTA
EST: gi|6031284|gb|AW076291.1|AW076291
EST:     TGTTGGACACACCACCACCTGGCTTGGATGAAGCAATTGCAATTTCTAAG                         GTTATGCAATTCCTTGAAGCACAAGAATACAGCATGTTTAGTCGCATTGTA
genomic: TGTTGGACACACCACCACCTGGCTTGGATGAAGCAATTGCAATTTCTAAGgtaagaagga ... tgtctctcagGTTATGCAATTCCTTGAAGCACAAGAATACAGCATGTTTAGTCGCATTGTA
EST: gi|5296253|gb|AI782933.1|AI782933
EST:     TGTTGGACACACCACCACCTGGCTTGGATGAAGCAATTGCAATTTCTAAG                         GTTATGCAATTCCTTGAAGCACAAGAATACAGCATGTTTAGTCGCATTGTA
genomic: TGTTGGACACACCACCACCTGGCTTGGATGAAGCAATTGCAATTTCTAAGgtaagaagga ... tgtctctcagGTTATGCAATTCCTTGAAGCACAAGAATACAGCATGTTTAGTCGCATTGTA
EST: gi|211363054|gb|FL031142.1|FL031142
EST:     TGTTGGACACACCACCACCTGGCTTGGATGAAGCAATTGCAATTTCTAAG                         GTGATGCAATTCCTTGAAGCACAAGAATACAGCATGTTTAGTCGCATTGTA
genomic: TGTTGGACACACCACCACCTGGCTTGGATGAAGCAATTGCAATTTCTAAGgtaagaagga ... tgtctctcagGTTATGCAATTCCTTGAAGCACAAGAATACAGCATGTTTAGTCGCATTGTA
EST: gi|148962847|gb|EE013769.2|EE013769
EST:     TGTTGGACACACCACCACCTGGCTTGGATGAAGCAATTGCAATTTCTAAG                         GTTATGCAATTCCTTGAAGCACAAGAATACAGCATGTTTAGTCGCATTGTA
genomic: TGTTGGACACACCACCACCTGGCTTGGATGAAGCAATTGCAATTTCTAAGgtaagaagga ... tgtctctcagGTTATGCAATTCCTTGAAGCACAAGAATACAGCATGTTTAGTCGCATTGTA
EST: gi|6973390|gb|AW438084.1|AW438084
EST:     TGTTGGACACACCACCACCTGGCTTGGATGAAGCAATTGCAATTTCTAAG                         GTTATGCAATTCCTTGAAGCACAAGAATACAGCATGTTTAGTCGCATTGTA
genomic: TGTTGGACACACCACCACCTGGCTTGGATGAAGCAATTGCAATTTCTAAGgtaagaagga ... tgtctctcagGTTATGCAATTCCTTGAAGCACAAGAATACAGCATGTTTAGTCGCATTGTA
EST: gi|18385084|gb|BM418283.1|BM418283
EST:     TGTTGGACACACCACCACCTGGCTTGGATGAAGCAATTGCAATTTCTAAG                         GTTATGCAATTCCTTGAAGCACAAGAATACAGCATGTTTAGTCGCATTGTA
genomic: TGTTGGACACACCACCACCTGGCTTGGATGAAGCAATTGCAATTTCTAAGgtaagaagga ... tgtctctcagGTTATGCAATTCCTTGAAGCACAAGAATACAGCATGTTTAGTCGCATTGTA
EST: gi|87152689|gb|DY397478.1|DY397478
EST:     TGTTGGACACACCACCACCTGGCTTGGATGAAGCAATTGCAATTTCTAAG                         GTTATGCAATTCCTTGAAGCACAAGAATACAGCATGTTTAGTCGCATTGTA
genomic: TGTTGGACACACCACCACCTGGCTTGGATGAAGCAATTGCAATTTCTAAGgtaagaagga ... tgtctctcagGTTATGCAATTCCTTGAAGCACAAGAATACAGCATGTTTAGTCGCATTGTA
EST: gi|22489513|gb|BU049436.1|BU049436
EST:     TGTTGGACACACCACCACCTGGCTTGGATGAAGCAATTGCAATTTCTAAG                         GTTATGCAATTCCTTGAAGCACAAGAATACAGCATGTTTAGTCTCTTTGTA
genomic: TGTTGGACACACCACCACCTGGCTTGGATGAAGCAATTGCAATTTCTAAGgtaagaagga ... tgtctctcagGTTATGCAATTCCTTGAAGCACAAGAATACAGCATGTTTAGTCGCATTGTA

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: 64

CTTGGAGAGTTAAAATTGGGGGAATTGTTGGACACACCACCACCTGGCTTGGATGAAGCAATTGCAATTTCTAAGgtaagaagga ... tgtctctcagGTTATGCAATTCCTTGAAGCACAAGAATACAGCATGTTTAGTCGCATTGTATTTGACACTGCCCCTACG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 168

CTTGGAGAGTTAAAATTGGGGGAATTGTTGGACACACCACCACCTGGCTTGGATGAAGCAATTGCAATTTCTAAGgtaagaagga ... tgtctctcagGTTATGCAATTCCTTGAAGCACAAGAATACAGCATGTTTAGTCGCATTGTATTTGACACTGCCCCTACG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 76

CTTGGAGAGTTAAAATTGGGGGAATTGTTGGACACACCACCACCTGGCTTGGATGAAGCAATTGCAATTTCTAAGgtaagaagga ... tgtctctcagGTTATGCAATTCCTTGAAGCACAAGAATACAGCATGTTTAGTCGCATTGTATTTGACACTGCCCCTACG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 96

CTTGGAGAGTTAAAATTGGGGGAATTGTTGGACACACCACCACCTGGCTTGGATGAAGCAATTGCAATTTCTAAGgtaagaagga ... tgtctctcagGTTATGCAATTCCTTGAAGCACAAGAATACAGCATGTTTAGTCGCATTGTATTTGACACTGCCCCTACG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ctgcttatcattcctctgattgtagtttgtgacctccatgttgcgtgtctctcagGTTATGCAATTCCTTGAAGCACAAGAATACAGCATGTTTAGTCGCATTGTATTTGACACTGCCCCTACG
             ctctgat  putative branch site (score: 96)
                                             tgtctctc  putative PPT
     tatcatt  TA-rich tract