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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tagcggcgtgagctatcctccactaattaataattatcatttcaactccatgaatcatctgcctttgtactggtgactaattatcgtttcctggcctcagGGTATCTTCACTGGAAGCTGTGGAACAGCGCTGGACCATGGTGTCACGGCCGTCGGCTACGGGACAGAGAACGGCAAGGACTACTGGATCGTGAAGAACT

Basic information

species Zea mays
transcript GRMZM2G166281_T01
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G166281_T01 (Zea mays), 3'ss of exon 3
lower sequence: Vv18s0001g09990.t01 (Vitis vinifera), 3'ss of exon 3
tagcggcgtgagctatcctccactaattaataattatcatttcaactccatgaatcatctgcctttgta--ctggtgactaattatcgtttcctggcctc---agGGTATCTTCACTGGAAGCTGTGGAACAGCGCTGGACCATGGTGTCACGGCCGTCGGCTACGGGACAGAGAACGGCAAGGACTACTGGATCGTGAAGAACT
        |   ||     |   |  ||     | ||| | |     |||||||  |  ||||||| ||   ||||   |  |  | ||||||    |||   ||||||| || |||||||| ||||| ||||| |||||||||||||| || || || || || || ||||| || ||   ||| |||||||| || |||||||
----aagttatactgagaacagtttcttccatgtgatcctgttg-taccatgaaatagttgcctttctaacttggttctttttatttgtttcccaatctcttcagGGTATATTTACTGGAAGATGTGGGACAGCACTGGACCATGGTGTTACTGCTGTTGGATATGGCACAGAAAATGGTGTGGATTACTGGATTGTAAAGAACT
















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|16920327|gb|BM074601.1|BM074601
EST:     TCAGTGTCGCAATTGAGGCTGCTGGCACAGCATTTCAGCTCTACAGCTCG                         GGTATCTTCACTGGAAGCTGTGGAACAGCGCTGGACCATGGTGTCACGGCC
genomic: TCAGTGTCGCAATTGAGGCTGCTGGCACAGCATTTCAGCTCTACAGCTCGgtaattggcg ... ctggcctcagGGTATCTTCACTGGAAGCTGTGGAACAGCGCTGGACCATGGTGTCACGGCC
EST: gi|13515985|gb|BG518261.1|BG518261
EST:     TCAGTGTCGCAATTGAGGCTGCTGGCACAGCATTTCAGCTCTACAGCTCG                         GGTATCTTCACTGGAAGCTGTGGAACAGCGCTGGACCATGGTGTCACGGCC
genomic: TCAGTGTCGCAATTGAGGCTGCTGGCACAGCATTTCAGCTCTACAGCTCGgtaattggcg ... ctggcctcagGGTATCTTCACTGGAAGCTGTGGAACAGCGCTGGACCATGGTGTCACGGCC
EST: gi|32923037|gb|CF027849.1|CF027849
EST:     TCAGTGTCGCAATTGAGGCTGCTGGCACAGCATTTCAGCTCTACAGCTCG                         GGTATCTTCACTGGAAGCTGTGGAACAGCGCTGGACCATGGTGTCACGGCC
genomic: TCAGTGTCGCAATTGAGGCTGCTGGCACAGCATTTCAGCTCTACAGCTCGgtaattggcg ... ctggcctcagGGTATCTTCACTGGAAGCTGTGGAACAGCGCTGGACCATGGTGTCACGGCC
EST: gi|18649519|gb|BM498338.1|BM498338
EST:     TCAGTGTCGCAATTGAGGCTGCTGGCACAGCATTTCAGCTCTACAGCTCG                         GGTATCTTCACTGGAAGCTGTGGAACAGCGCTGGACCATGGTGTCACGGCC
genomic: TCAGTGTCGCAATTGAGGCTGCTGGCACAGCATTTCAGCTCTACAGCTCGgtaattggcg ... ctggcctcagGGTATCTTCACTGGAAGCTGTGGAACAGCGCTGGACCATGGTGTCACGGCC
EST: gi|18170436|gb|BM340276.1|BM340276
EST:     TCAGTGTCGCAATTGAGGCTGCTGGCACAGCATTTCAGCTCTACAGCTCG                         GGTATCTTCACTGGAAGCTGTGGAACAGCGCTGGACCATGGTGTCACGGCC
genomic: TCAGTGTCGCAATTGAGGCTGCTGGCACAGCATTTCAGCTCTACAGCTCGgtaattggcg ... ctggcctcagGGTATCTTCACTGGAAGCTGTGGAACAGCGCTGGACCATGGTGTCACGGCC
EST: gi|32923298|gb|CF028110.1|CF028110
EST:     TCAGTGTCGCAATTGAGGCTGCTGGCACAGCATTTCAGCTCTACAGCTCG                         GGTATCTTCACTGGAAGCTGTGGAACAGCGCTGGACCATGGTGTCACGGCC
genomic: TCAGTGTCGCAATTGAGGCTGCTGGCACAGCATTTCAGCTCTACAGCTCGgtaattggcg ... ctggcctcagGGTATCTTCACTGGAAGCTGTGGAACAGCGCTGGACCATGGTGTCACGGCC
EST: gi|7958403|gb|AW862705.1|AW862705
EST:     TCAGTGTCGCAATTGAGGCTGCTGGCACAGCATTTCAGCTCTACAGCTCG                         GGTATATTCACTGGAAGCTGTGGAACAGCGCTGGACCATGGTGTCACGGCC
genomic: TCAGTGTCGCAATTGAGGCTGCTGGCACAGCATTTCAGCTCTACAGCTCGgtaattggcg ... ctggcctcagGGTATCTTCACTGGAAGCTGTGGAACAGCGCTGGACCATGGTGTCACGGCC
EST: gi|32843840|gb|CD983521.1|CD983521
EST:     TCAGTGTCGCAATTGAGGCTGCTGGCACAGCATTTCAGCTCTACAGCTCG                         GGTATCTTCACTGGAAGCTGTGGAACAGCGCTGGACCATGGTGTCACGGCC
genomic: TCAGTGTCGCAATTGAGGCTGCTGGCACAGCATTTCAGCTCTACAGCTCGgtaattggcg ... ctggcctcagGGTATCTTCACTGGAAGCTGTGGAACAGCGCTGGACCATGGTGTCACGGCC
EST: gi|71444254|gb|DR825304.1|DR825304
EST:     TCAGTGTCGCAATTGAGGCTGCTGGCACAGCATTTCAGCTCTACAGCTCG                         GGTATCTTCACTGGAAGCTGTGGAACAGCGCTGGACCATGGTGTCACGGCC
genomic: TCAGTGTCGCAATTGAGGCTGCTGGCACAGCATTTCAGCTCTACAGCTCGgtaattggcg ... ctggcctcagGGTATCTTCACTGGAAGCTGTGGAACAGCGCTGGACCATGGTGTCACGGCC
EST: gi|18172588|gb|BM347976.1|BM347976
EST:     TCAGTGTCGCAATTGAGGCTGCTGGCACAGCATTTCAGCTCTACAGCTCG                         GGTATCTTCACTGGAAGCTGTGGAACAGCGCTGGACCATGGTGTCACGGCC
genomic: TCAGTGTCGCAATTGAGGCTGCTGGCACAGCATTTCAGCTCTACAGCTCGgtaattggcg ... ctggcctcagGGTATCTTCACTGGAAGCTGTGGAACAGCGCTGGACCATGGTGTCACGGCC
EST: gi|8102925|gb|AW927598.1|AW927598
EST:     TCAGTGTCGCAATTGAGGCTGCTGGCACAGCATTTCAGCTCTACAGCTCG                         GGTATATTCACTGGAAGCTGTGGAACAGCGCTGGACCATGGTGTCACGGCC
genomic: TCAGTGTCGCAATTGAGGCTGCTGGCACAGCATTTCAGCTCTACAGCTCGgtaattggcg ... ctggcctcagGGTATCTTCACTGGAAGCTGTGGAACAGCGCTGGACCATGGTGTCACGGCC
EST: gi|13490779|gb|BG517543.1|BG517543
EST:     GCAATTGAGGCTGCTGGCACAGCATTTCAGCTCTACAGCTCG                         GGTATCTTCACTGGAAGCTGTGGAACAGCGCTGGACCATGGTGTCACGGCC
genomic: GCAATTGAGGCTGCTGGCACAGCATTTCAGCTCTACAGCTCGgtaattggcg ... ctggcctcagGGTATCTTCACTGGAAGCTGTGGAACAGCGCTGGACCATGGTGTCACGGCC
EST: gi|22489668|gb|BU049578.1|BU049578
EST:     TCAGTGTCGCAATTGAGGCTGCTGGCACAGCATTTCAGCTCTACAGCTCG                         GGTATCTTCACTGGAAGCTGTGGAACAGCGCTGGACCATGGTGTCACGGCC
genomic: TCAGTGTCGCAATTGAGGCTGCTGGCACAGCATTTCAGCTCTACAGCTCGgtaattggcg ... ctggcctcagGGTATCTTCACTGGAAGCTGTGGAACAGCGCTGGACCATGGTGTCACGGCC
EST: gi|211384516|gb|FL378678.1|FL378678
EST:     AGTGTCGCAATTTGAG-CTGGCTG-CACAGCATTTCAGCTCTACAGCTCG                         GGTATCTTCACTGGGAGCTGTG
genomic: AGTGTCGCAATT-GAGGCTG-CTGGCACAGCATTTCAGCTCTACAGCTCGgtaattggcg ... ctggcctcagGGTATCTTCACTGGAAGCTGTG

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: 203

ACCAGCGAACGATGAGAAGAGTCTGCAGAAGGCAGTTGCAAACCAGCCTGTCAGTGTCGCAATTGAGGCTGCTGGCACAGCATTTCAGCTCTACAGCTCGgtaattggcg ... ctggcctcagGGTATCTTCACTGGAAGCTGTGGAACAGCGCTGGACCATGGTGTCACGGCCGTCGGCTACGGGACAGAGAACGGCAAGGACTACTGGATCGTGAAGAACT


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 1098

ACCAGCGAACGATGAGAAGAGTCTGCAGAAGGCAGTTGCAAACCAGCCTGTCAGTGTCGCAATTGAGGCTGCTGGCACAGCATTTCAGCTCTACAGCTCGgtaattggcg ... ctggcctcagGGTATCTTCACTGGAAGCTGTGGAACAGCGCTGGACCATGGTGTCACGGCCGTCGGCTACGGGACAGAGAACGGCAAGGACTACTGGATCGTGAAGAACT


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 1065

ACCAGCGAACGATGAGAAGAGTCTGCAGAAGGCAGTTGCAAACCAGCCTGTCAGTGTCGCAATTGAGGCTGCTGGCACAGCATTTCAGCTCTACAGCTCGgtaattggcg ... ctggcctcagGGTATCTTCACTGGAAGCTGTGGAACAGCGCTGGACCATGGTGTCACGGCCGTCGGCTACGGGACAGAGAACGGCAAGGACTACTGGATCGTGAAGAACT


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 958

ACCAGCGAACGATGAGAAGAGTCTGCAGAAGGCAGTTGCAAACCAGCCTGTCAGTGTCGCAATTGAGGCTGCTGGCACAGCATTTCAGCTCTACAGCTCGgtaattggcg ... ctggcctcagGGTATCTTCACTGGAAGCTGTGGAACAGCGCTGGACCATGGTGTCACGGCCGTCGGCTACGGGACAGAGAACGGCAAGGACTACTGGATCGTGAAGAACT




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ctccatgaatcatctgcctttgtactggtgactaattatcgtttcctggcctcagGGTATCTTCACTGGAAGCTGTGGAACAGCGCTGGACCATGGTGTCACGGCCGTCGGCTACGGGACAGAGAACGGCAAGGACTACTGGATCGTGAAGAACT
                             gactaat  putative branch site (score: 958)
                                      tcgtttcct  putative PPT
                              actaattat  TA-rich tract
















Putative cis-regulatory sequences

 atgc intron ATGC exonic elements by Pertea et al.
 ATGC exon atgc putative intronic elements
 ATGC putative exonic elements identified for retained introns
        10        20        30        40        50        60        70        80        90        100       110       120       130       140       150       160       170       180       190       200       210       220 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tagcggcgtgagctatcctccactaattaataattatcatttcaactccatgaatcatctgcctttgtactggtgactaattatcgtttcctggcctcagGGTATCTTCACTGGAAGCTGTGGAACAGCGCTGGACCATGGTGTCACGGCCGTCGGCTACGGGACAGAGAACGGCAAGGACTACTGGATCGTGAAGAACT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAC
- - - - - - - - cctccac
- - - - - - - - - - - - - - - - - - - - - - -ctccatg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ctggtga