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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...cgggtgtcatctgagatttcccgagaaataaattgcgtgatgaaagcaaatcagttgccagtctgtgttaacagttatataagatacatgtctattgcagGTGGATCCAAACACTGGGGTCGCCATGTATGAATCAGATGACATCATAAAATACCTAGCTGACACATATG

Basic information

species Zea mays
transcript GRMZM2G085000_T03
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G085000_T03 (Zea mays), 3'ss of exon 4
lower sequence: LOC_Os08g44400.3 (Oryza sativa), 3'ss of exon 5
-cgggtgtcatctgagatttcccgagaaataaattgcgtgatgaaagcaaatcagttgccagtctgtgttaacagttatataagatacatgtctattgcagGTGGATCCAAACACTGGGGTCGCCATGTATGAATCAGATGACATCATAAAATACCTAGCTGACACATATG
       |||  |  ||| |   |          ||  ||    ||| |  |  |    |||| ||| || |   | || |||| |||   | |  ||||||||||||||||||| ||||| |||||||||||||| |||| ||||||||||||||| || |||| |||||
tttcccttcacttaggatatttgggtgttctttctgtctggaagaagtag-tgtgaaatcagtttgtttttatcatcatctaaggtactcttatgctgcagGTGGATCCAAACACAGGGGTTGCCATGTATGAATCTGATGCCATCATAAAATACCTGGCCGACAAATATG

upper sequence: GRMZM2G085000_T03 (Zea mays), 3'ss of exon 4
lower sequence: Vv08s0007g03250.t01 (Vitis vinifera), 3'ss of exon 5
cgggtgtcatctgagattt--cccgagaaataaattgcgtgatgaaagcaaatcagttgccagtctgtgttaacagttatataagatacatgtctattgcagGTGGATCCAAACACTGGGGTCGCCATGTATGAATCAGATGACATCATAAAATACCTAGCTGACACATATG
 |  | || |   | ||    ||   | | ||||     | ||| |           | | |    ||| |||  | |  | ||  |   |    | ||||||||||||||||||| || || || ||||||||||| |||||||| || || ||  | | ||  | |||||
tgcatctcttaaaacatcaagcctttggattaaagcttattatgcacaaggggtgcgtccaaacaggtgctaa--gcttcaaaattttgtttctaagtgcagGTGGATCCAAACACAGGAGTTGCAATGTATGAATCGGATGACATAATTAAGTATTTGGTTGGGAAATATG
















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|60352714|gb|DN219687.1|DN219687
EST:     GTTTCCTTACATG                         GTGGATCCAAACACTGGGGTCGCCATGTATGAATCAGATGACATCATAAAA
genomic: GTTTCCTTACATGgtatgcaacc ... tctattgcagGTGGATCCAAACACTGGGGTCGCCATGTATGAATCAGATGACATCATAAAA
EST: gi|211469259|gb|FL411595.1|FL411595
EST:     TCCGACCTAAAGTCCTTGAAATGGGTGGAAAGAAACAGTTTCCTTACATG                         GTGGATCCAAACACTGGGGTCGYCATGTATGAATCAGATGACATCATAAAA
genomic: TCCGACCTAAAGTCCTTGAAATGGGTGGAAAGAAACAGTTTCCTTACATGgtatgcaacc ... tctattgcagGTGGATCCAAACACTGGGGTCGCCATGTATGAATCAGATGACATCATAAAA
EST: gi|60356894|gb|DN223867.1|DN223867
EST:     TCCGACCTAAAGTCCTTGAAATGGGTGGAAAGAAACAGTTTCCTTACATG                         GTGGATCCAAACACTGGGGTCGCCATGTATGAATCAGATGACATCATAAAA
genomic: TCCGACCTAAAGTCCTTGAAATGGGTGGAAAGAAACAGTTTCCTTACATGgtatgcaacc ... tctattgcagGTGGATCCAAACACTGGGGTCGCCATGTATGAATCAGATGACATCATAAAA
EST: gi|40303424|gb|CK347811.1|CK347811
EST:     GGAAAGAAACAGTTTCCTTACATG                         GTGGATCCAAACACTGGGGTCGCCATGTATGAATCAGATGACATCATAAAA
genomic: GGAAAGAAACAGTTTCCTTACATGgtatgcaacc ... tctattgcagGTGGATCCAAACACTGGGGTCGCCATGTATGAATCAGATGACATCATAAAA
EST: gi|93282046|gb|EB674310.1|EB674310
EST:     TCCGACCTAAAGTCCTTGAAATGGGTGGAAAGAAACAGTTTCCTTACATG                         GTGGATCCAAACACTGGGGTCGCCATGTATGAATCAGATGACATCATAAAA
genomic: TCCGACCTAAAGTCCTTGAAATGGGTGGAAAGAAACAGTTTCCTTACATGgtatgcaacc ... tctattgcagGTGGATCCAAACACTGGGGTCGCCATGTATGAATCAGATGACATCATAAAA
EST: gi|32917029|gb|CF021841.1|CF021841
EST:     TCCGACCTAAAGTCCTTGAAATGGGTGGAAAGAAACAGTTTCCTTACATG                         GTGGATCCAAACACTGGGGTCGCCATGTATGAATCAGATGACATCATAAAA
genomic: TCCGACCTAAAGTCCTTGAAATGGGTGGAAAGAAACAGTTTCCTTACATGgtatgcaacc ... tctattgcagGTGGATCCAAACACTGGGGTCGCCATGTATGAATCAGATGACATCATAAAA

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), 42 (downstream exon)
Score: 88

CTTGGACCTAGATGTACTATTTTACCCCTGTCCTCGAAAAGGCCCAACATTCCGACCTAAAGTCCTTGAAATGGGTGGAAAGAAACAGTTTCCTTACATGgtatgcaacc ... tctattgcagGTGGATCCAAACACTGGGGTCGCCATGTATGAATCAGATGACATCATAAAATACCTAGCTGACACATATG


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 169

CTTGGACCTAGATGTACTATTTTACCCCTGTCCTCGAAAAGGCCCAACATTCCGACCTAAAGTCCTTGAAATGGGTGGAAAGAAACAGTTTCCTTACATGgtatgcaacc ... tctattgcagGTGGATCCAAACACTGGGGTCGCCATGTATGAATCAGATGACATCATAAAATACCTAGCTGACACATATG


Block sizes: 49 (upstream exon), 42 (downstream exon)
Score: 151

CTTGGACCTAGATGTACTATTTTACCCCTGTCCTCGAAAAGGCCCAACATTCCGACCTAAAGTCCTTGAAATGGGTGGAAAGAAACAGTTTCCTTACATGgtatgcaacc ... tctattgcagGTGGATCCAAACACTGGGGTCGCCATGTATGAATCAGATGACATCATAAAATACCTAGCTGACACATATG


Block sizes: 44 (upstream exon), 42 (downstream exon)
Score: 52

CTTGGACCTAGATGTACTATTTTACCCCTGTCCTCGAAAAGGCCCAACATTCCGACCTAAAGTCCTTGAAATGGGTGGAAAGAAACAGTTTCCTTACATGgtatgcaacc ... tctattgcagGTGGATCCAAACACTGGGGTCGCCATGTATGAATCAGATGACATCATAAAATACCTAGCTGACACATATG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gcaaatcagttgccagtctgtgttaacagttatataagatacatgtctattgcagGTGGATCCAAACACTGGGGTCGCCATGTATGAATCAGATGACATCATAAAATACCTAGCTGACACATATG
                    tgttaac  putative branch site (score: 52)
                      ttaacagttatataa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
cgggtgtcatctgagatttcccgagaaataaattgcgtgatgaaagcaaatcagttgccagtctgtgttaacagttatataagatacatgtctattgcagGTGGATCCAAACACTGGGGTCGCCATGTATGAATCAGATGACATCATAAAATACCTAGCTGACACATATG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTGA