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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagtaaagttttcaatacatacgaaatggtcctgtattgttcttatatatataatatatgtgcaagtttttcctttcttgatgatcatagtactacactactaataattcagaaagtttgagcattattattgcttccattctacgtgcagTTATATTCACCCCATCTAGATACAGCACCCCCCAGATGGGTTCACCTTGCTCATGGACTGCTTCTCTTTCTTTATCAG

Basic information

species Zea mays
transcript GRMZM2G466281_T02
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G466281_T02 (Zea mays), 3'ss of exon 3
lower sequence: LOC_Os02g02750.3 (Oryza sativa), 3'ss of exon 3
gtaagtaaagttttcaatacatacgaaatggtcctgtattgttcttatatatataatatatgtgcaagtttttcctttcttgatgatcatagtactacactactaataattcagaaagtttgagcattattattgcttccattctacgtgcagTTATATTCACCCCATCTAGATACAGCACCCCCCAGATGGGTTCACCTTGCTCATGGACTGCTTCTCTTTCTTTATCAG
    |||| || |   ||   |   || |  | |  |  | |  ||||   | |    |||    | |  |||  || || | ||||          ||  |  |||| |||||  |  |    | |||||| || | | ||| ||  ||||||| ||||| || ||||| ||||||||||| || |||||||| |||||||| |||||| |||||||||| ||||| |||
----gtaa-gtatcttatggctgtaaatt--ttcgatgctttctttat---tgtggcctatacagaggagttttattgctcgttgat---------gcagcagaaatatttcagccaactgataccttattactgttccaattttatctgcagTTTTATTCCCCTCATCTCGATACAGCACCACCTAGATGGGTGCACCTTGCACATGGAATGCTTCTCTTCCTTTACCAG
















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|211250318|gb|FL201841.1|FL201841
EST:     TTACACTGACAGGTTTCATGTTTCTACTGACATCAGCATTCCTTGGCTTT                         TTATATTCACCCCATCTAGATACAGCGCCCCCCAGATGGGTTCA
genomic: TTACACTGACAGGTTTCATGTTTCTACTGACATCAGCATTCCTTGGCTTTgtaagtaaag ... ctacgtgcagTTATATTCACCCCATCTAGATACAGCACCCCCCAGATGGGTTCA
EST: gi|101388019|gb|EB816024.1|EB816024
EST:     TTACACTGACAGGTTTCATGTTTCTACTGACATCAGCATTCCTTGGCTTT                         TTATATTCACCCCATCTAGATACAGCACCCCCCAGATGGGTTCACCTTGCT
genomic: TTACACTGACAGGTTTCATGTTTCTACTGACATCAGCATTCCTTGGCTTTgtaagtaaag ... ctacgtgcagTTATATTCACCCCATCTAGATACAGCACCCCCCAGATGGGTTCACCTTGCT
EST: gi|76933447|gb|DV173462.1|DV173462
EST:     TTACACTGACAGGTTTCATGTTTCTACTGACATCAGCATTCCTTGGCTTT                         TTATATTCACCCCATCTAGATACAGCACCCCCCAGATGGGTTCACCTTGCT
genomic: TTACACTGACAGGTTTCATGTTTCTACTGACATCAGCATTCCTTGGCTTTgtaagtaaag ... ctacgtgcagTTATATTCACCCCATCTAGATACAGCACCCCCCAGATGGGTTCACCTTGCT
EST: gi|78108358|gb|DV526776.1|DV526776
EST:     TTACACTGACAGGTTTCATGTTTCTACTGACATCAGCATTCCTTGGCTTT                         TTATATTCACCCCATCTAGATACAGCACCCCCCAGATGGGTTCACCTTGCT
genomic: TTACACTGACAGGTTTCATGTTTCTACTGACATCAGCATTCCTTGGCTTTgtaagtaaag ... ctacgtgcagTTATATTCACCCCATCTAGATACAGCACCCCCCAGATGGGTTCACCTTGCT
EST: gi|76284393|gb|DV023961.1|DV023961
EST:     TTACACTGACAGGTTTCATGTTTCTACTGACATCAGCATTCCTTGGCTTT                         TTATATTCACCCCATCTAGATACAGCACCCCCCAGATGGGTTCACCTTGCT
genomic: TTACACTGACAGGTTTCATGTTTCTACTGACATCAGCATTCCTTGGCTTTgtaagtaaag ... ctacgtgcagTTATATTCACCCCATCTAGATACAGCACCCCCCAGATGGGTTCACCTTGCT
EST: gi|211250321|gb|FL201844.1|FL201844
EST:     TTACACTGACAGGTTTCATGTTTCTACTGACATCAGCATTCCTTGGCTTT                         TTATATTCACCCCATCTAGAT
genomic: TTACACTGACAGGTTTCATGTTTCTACTGACATCAGCATTCCTTGGCTTTgtaagtaaag ... ctacgtgcagTTATATTCACCCCATCTAGAT
EST: gi|148930548|gb|EE285169.2|EE285169
EST:     TTACACTGACAGGTTTCATGTTTCTACTGACATCAGCATTCCTTGGCTTT                         TTATATTCACCCCATCTAGATACAGCACCCCCCAGATGGGTTCACCTTGCT
genomic: TTACACTGACAGGTTTCATGTTTCTACTGACATCAGCATTCCTTGGCTTTgtaagtaaag ... ctacgtgcagTTATATTCACCCCATCTAGATACAGCACCCCCCAGATGGGTTCACCTTGCT
EST: gi|148948015|gb|EC893516.2|EC893516
EST:     TTACACTGACAGGTTTCATGTTTCTACTGACATCAGCATTCCTTGGCTTT                         TTATATTCACCCCATCTAGATACAGCACCCCCCAGATGGGTTCACCTTGCT
genomic: TTACACTGACAGGTTTCATGTTTCTACTGACATCAGCATTCCTTGGCTTTgtaagtaaag ... ctacgtgcagTTATATTCACCCCATCTAGATACAGCACCCCCCAGATGGGTTCACCTTGCT
EST: gi|211250319|gb|FL201842.1|FL201842
EST:     TTACACTGACAGGTTTCATGTTTCTACTGACATCAGCATTCCTTGGCTTT                         TTATATTCACCCCATCTAGATACAGCACCCCCCAGATGGGTTCACCTTGCT
genomic: TTACACTGACAGGTTTCATGTTTCTACTGACATCAGCATTCCTTGGCTTTgtaagtaaag ... ctacgtgcagTTATATTCACCCCATCTAGATACAGCACCCCCCAGATGGGTTCACCTTGCT
EST: gi|149085392|gb|EE174899.2|EE174899
EST:     TTACACTGACAGGTTTCATGTTTCTACTGACATCAGCATTCCTTGGCTTT                         TTATATTCACCCCATCTAGATACAGCACCCCCCAGATGGGTTCACCTTGCT
genomic: TTACACTGACAGGTTTCATGTTTCTACTGACATCAGCATTCCTTGGCTTTgtaagtaaag ... ctacgtgcagTTATATTCACCCCATCTAGATACAGCACCCCCCAGATGGGTTCACCTTGCT
EST: gi|88756189|gb|DY540330.1|DY540330
EST:     TTACACTGACAGGTTTCATGTTTCTACTGACATCAGCATTCCTTGGCTTT                         TTATATTCACCCCATCTAGATACAGCACCCCCCAGATGGGTTCACCTTGCT
genomic: TTACACTGACAGGTTTCATGTTTCTACTGACATCAGCATTCCTTGGCTTTgtaagtaaag ... ctacgtgcagTTATATTCACCCCATCTAGATACAGCACCCCCCAGATGGGTTCACCTTGCT
EST: gi|88756155|gb|DY540296.1|DY540296
EST:     TTACACTGACAGGTTTCATGTTTCTACTGACATCAGCATTCCTTGGCTTT                         TTATATTCACCCCATCTAGATACAGCACCCCCCAGATGGGTTCACCTTGCT
genomic: TTACACTGACAGGTTTCATGTTTCTACTGACATCAGCATTCCTTGGCTTTgtaagtaaag ... ctacgtgcagTTATATTCACCCCATCTAGATACAGCACCCCCCAGATGGGTTCACCTTGCT
EST: gi|211250316|gb|FL201839.1|FL201839
EST:     TTACACTGACAGGTTTCATGTTTCTACTGACATCAGCATTCCTTGGCTTT                         TTATATTCACCCCATCTAGATACAGCACCCCCCAGATGGGTTCACCTTGCT
genomic: TTACACTGACAGGTTTCATGTTTCTACTGACATCAGCATTCCTTGGCTTTgtaagtaaag ... ctacgtgcagTTATATTCACCCCATCTAGATACAGCACCCCCCAGATGGGTTCACCTTGCT

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: 48 (upstream exon), 49 (downstream exon)
Score: 329

ATTACACTGACAGGTTTCATGTTTCTACTGACATCAGCATTCCTTGGCTTTgtaagtaaag ... ctacgtgcagTTATATTCACCCCATCTAGATACAGCACCCCCCAGATGGGTTCACCTTGCTCATGGACTGCTTCTCTTTCTTTATCAG


Block sizes: 47 (upstream exon), 49 (downstream exon)
Score: 281

ATTACACTGACAGGTTTCATGTTTCTACTGACATCAGCATTCCTTGGCTTTgtaagtaaag ... ctacgtgcagTTATATTCACCCCATCTAGATACAGCACCCCCCAGATGGGTTCACCTTGCTCATGGACTGCTTCTCTTTCTTTATCAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 211

ATTACACTGACAGGTTTCATGTTTCTACTGACATCAGCATTCCTTGGCTTTgtaagtaaag ... ctacgtgcagTTATATTCACCCCATCTAGATACAGCACCCCCCAGATGGGTTCACCTTGCTCATGGACTGCTTCTCTTTCTTTATCAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 501

ATTACACTGACAGGTTTCATGTTTCTACTGACATCAGCATTCCTTGGCTTTgtaagtaaag ... ctacgtgcagTTATATTCACCCCATCTAGATACAGCACCCCCCAGATGGGTTCACCTTGCTCATGGACTGCTTCTCTTTCTTTATCAG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

actactaataattcagaaagtttgagcattattattgcttccattctacgtgcagTTATATTCACCCCATCTAGATACAGCACCCCCCAGATGGGTTCACCTTGCTCATGGACTGCTTCTCTTTCTTTATCAG
  tactaat  putative branch site (score: 501)
                                     cttccattct  putative PPT
     taataattcagaaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaagtaaagttttcaatacatacgaaatggtcctgtattgttcttatatatataatatatgtgcaagtttttcctttcttgatgatcatagtactacactactaataattcagaaagtttgagcattattattgcttccattctacgtgcagTTATATTCACCCCATCTAGATACAGCACCCCCCAGATGGGTTCACCTTGCTCATGGACTGCTTCTCTTTCTTTATCAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CATGGA