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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatgtgtacagtgtattgcgctttcatcaaattatttgactggttatgttttcaaagtcacatgtttgctgcagtagattcttagttatcaataattatctccgttctacccagcaaaaatgtatccatttctttattacatctatcatagcctcataagaatttttgcagGGTGAAATACATCATGTCATGAACCCTGATCCTTATCGGGGGACTTTCGGGTCTGATGCTGCAGCTTATGCTAAGGAAGTCGAAGAACACATAACTTATG

Basic information

species Zea mays
transcript GRMZM2G124353_T01
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G124353_T01 (Zea mays), 3'ss of exon 3
lower sequence: LOC_Os03g07570.1 (Oryza sativa), 3'ss of exon 3
gtatgtgtacagtgtattgcgctttcatcaaattatttgactggttatgttttcaaagtcacatgtttgctgcagtagattcttagttatcaataattatctccgttctacccagcaaaaatgtatccatttctttattacatctatcatagcctcataagaatttttgcagGGTGAAATACATCATGTCATGAACCCTGATCCTTATCGGGGGACTTTCGGGTCTGATGCTGCAGCTTATGCTAAGGAAGTCGAAGAACACATAACTTATG
                                                                      ||  |   || ||      ||  | || | ||    |  |   || |  ||  ||  | ||   |    | ||  | || |  || || | ||  ||||||||| |||||||||||||||||||||||||||||||| || || |||||||| |||||||||| ||||||||| ||||||||||||||||| |||| |||||
----------------------------------------------------------------------tgtgggcaatgctagaaagtc--ttataacctgaaatggaggtagtagcaaactagtctttatctatgaaaatgaagcaaaatcttatcacaacatttgcagGGCGAAATACATCATGTCATGAACCCTGATCCTTACCGTGGAACTTTCGGTTCTGATGCTGTAGCTTATGCCAAGGAAGTCGAAGAACAAATAAATTATG
















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|149029600|gb|EE154752.2|EE154752
EST:     GTACGATTGGATTGACTGGTATGCAGACGTGGAAATACCCAATTCCTCAG                         GGTGAAATACATCATGTCATGAACCCTGATCCTT
genomic: GTACGATTGGATTGACTGGTATGCAGACGTGGAAATACCCAATTCCTCAGgtatgtgtac ... atttttgcagGGTGAAATACATCATGTCATGAACCCTGATCCTT
EST: gi|67034943|gb|CO463476.1|CO463476
EST:     GTACGATTGGATTGACTGGTTTGCAGACGTGGAAATACCCAATTCCTCAG                         GGTGAAATACATCATGTCATGAACCCTGATCCTTATCGGGGGACTTTCGGG
genomic: GTACGATTGGATTGACTGGTATGCAGACGTGGAAATACCCAATTCCTCAGgtatgtgtac ... atttttgcagGGTGAAATACATCATGTCATGAACCCTGATCCTTATCGGGGGACTTTCGGG
EST: gi|149042716|gb|EE047231.2|EE047231
EST:     GTACGATTGGATTGACTGGTATGCAGACGTGGAAATACCCAATTCCTCAG                         GGTGAAATACATCATGTCATGAACCCTGATCCTTATCGGGGGACTTTCGGG
genomic: GTACGATTGGATTGACTGGTATGCAGACGTGGAAATACCCAATTCCTCAGgtatgtgtac ... atttttgcagGGTGAAATACATCATGTCATGAACCCTGATCCTTATCGGGGGACTTTCGGG
EST: gi|211311887|gb|FK975958.1|FK975958
EST:     TGGATTGACTGGTTTGCAGACGTGGAAATACCCAATTCCTCAG                         GGTGAAATACATCATGTCATGAACCCTGATCCTTATCGGGGGACTTTCGGG
genomic: TGGATTGACTGGTATGCAGACGTGGAAATACCCAATTCCTCAGgtatgtgtac ... atttttgcagGGTGAAATACATCATGTCATGAACCCTGATCCTTATCGGGGGACTTTCGGG
EST: gi|148965746|gb|EE016621.2|EE016621
EST:     GTACGATTGGATTGACTGGTATGCAGACGTGGAAATACCCAATTCCTCAG                         GGTGAAATACATCATGTCATGAACCCTGATCCTTATCGGGGGACTTTCGGG
genomic: GTACGATTGGATTGACTGGTATGCAGACGTGGAAATACCCAATTCCTCAGgtatgtgtac ... atttttgcagGGTGAAATACATCATGTCATGAACCCTGATCCTTATCGGGGGACTTTCGGG
EST: gi|6626596|gb|AW258128.1|AW258128
EST:     GTACGATTGGATTGACTGGTTTGCAGACGTGGAAATACCCAATTCCTCAG                         GGTGAAATACATCATGTCATGAACCCTGATCCTTATCGGGGGACTTTCGGG
genomic: GTACGATTGGATTGACTGGTATGCAGACGTGGAAATACCCAATTCCTCAGgtatgtgtac ... atttttgcagGGTGAAATACATCATGTCATGAACCCTGATCCTTATCGGGGGACTTTCGGG
EST: gi|44682053|gb|CK787101.1|CK787101
EST:     TTGGATTGACTGGTATGCAGACGTGGAAATACCCAATTCCTCAG                         GGTGAAATACATCATGTCATGAACCCTGATCCTTATCGGGGGACTTTCGGG
genomic: TTGGATTGACTGGTATGCAGACGTGGAAATACCCAATTCCTCAGgtatgtgtac ... atttttgcagGGTGAAATACATCATGTCATGAACCCTGATCCTTATCGGGGGACTTTCGGG
EST: gi|94472312|gb|EB701270.1|EB701270
EST:     GTACGATTGGATTGACTGGTATGCAGACGTGGAAATACCCAATTCCTCAG                         GGTGAAATACATCATGTCATGAACCCTGATCCTTATCGGGGGACTTTCGGG
genomic: GTACGATTGGATTGACTGGTATGCAGACGTGGAAATACCCAATTCCTCAGgtatgtgtac ... atttttgcagGGTGAAATACATCATGTCATGAACCCTGATCCTTATCGGGGGACTTTCGGG
EST: gi|13558145|gb|BG549501.1|BG549501
EST:     GTACGATTGGATTGACTGGTATGCAGACGTGGAAATACCCAATTCCTCAG                         GGTGAAATACATCATGTCATGAACCCTGATCCTTATCGGGGGACTTTCGGG
genomic: GTACGATTGGATTGACTGGTATGCAGACGTGGAAATACCCAATTCCTCAGgtatgtgtac ... atttttgcagGGTGAAATACATCATGTCATGAACCCTGATCCTTATCGGGGGACTTTCGGG
EST: gi|148955020|gb|EC900523.2|EC900523
EST:     GTACGATTGGATTGACTGGTATGCAGACGTGGAAATACCCAATTCCTCAG                         GGTGAAATACATCATGTCATGAACCCTGATCCTTATCGGGGGACTTTCGGG
genomic: GTACGATTGGATTGACTGGTATGCAGACGTGGAAATACCCAATTCCTCAGgtatgtgtac ... atttttgcagGGTGAAATACATCATGTCATGAACCCTGATCCTTATCGGGGGACTTTCGGG
EST: gi|31910697|gb|CD651554.1|CD651554
EST:     GTACGATTGGATTGACTGGTATGCAGACGTGGAAATACCCAATTCCTCAG                         GGTGAAATACATCATGTCATGAACCCTGATCCTTATCGGGGGACTTTCGGG
genomic: GTACGATTGGATTGACTGGTATGCAGACGTGGAAATACCCAATTCCTCAGgtatgtgtac ... atttttgcagGGTGAAATACATCATGTCATGAACCCTGATCCTTATCGGGGGACTTTCGGG
EST: gi|31350579|gb|CD434936.1|CD434936
EST:     GTACGATTGGATTGACTGGTATGCAGACGTGGAAATACCCAATTCCTCAN                         GGTGAAATACATCATGTCATGAACCCTGATCCTTATCGGGGGACTTTCGGG
genomic: GTACGATTGGATTGACTGGTATGCAGACGTGGAAATACCCAATTCCTCAGgtatgtgtac ... atttttgcagGGTGAAATACATCATGTCATGAACCCTGATCCTTATCGGGGGACTTTCGGG
EST: gi|14208236|gb|BG841914.1|BG841914
EST:     GTACGATTGGATTGACTGGTATGCAGACGTGGAAATACCCAATTCCTCAG                         GGTGAAATACATCATGTCATGAACCCTGATCCTTATCGGGGGACTTTCGGG
genomic: GTACGATTGGATTGACTGGTATGCAGACGTGGAAATACCCAATTCCTCAGgtatgtgtac ... atttttgcagGGTGAAATACATCATGTCATGAACCCTGATCCTTATCGGGGGACTTTCGGG
EST: gi|148929128|gb|EC874538.2|EC874538
EST:     GTACGATTGGATTGACTGGTATGCAGACGTGGAAATACCCAATTCCTCAG                         GGGTGAAATACATCATGTCATGAACCCTGATCCTTATCGGGGGACTTTCGG
genomic: GTACGATTGGATTGACTGGTATGCAGACGTGGAAATACCCAATTCCTCAGgtatgtgtac ... atttttgcagGG-TGAAATACATCATGTCATGAACCCTGATCCTTATCGGGGGACTTTCGG

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: 487

GAATCTCAGTATGGTTGCGCTCAGAAATGCATATCATGGCGGAAGTGCCGGTACGATTGGATTGACTGGTATGCAGACGTGGAAATACCCAATTCCTCAGgtatgtgtac ... atttttgcagGGTGAAATACATCATGTCATGAACCCTGATCCTTATCGGGGGACTTTCGGGTCTGATGCTGCAGCTTATGCTAAGGAAGTCGAAGAACACATAACTTATG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 715

GAATCTCAGTATGGTTGCGCTCAGAAATGCATATCATGGCGGAAGTGCCGGTACGATTGGATTGACTGGTATGCAGACGTGGAAATACCCAATTCCTCAGgtatgtgtac ... atttttgcagGGTGAAATACATCATGTCATGAACCCTGATCCTTATCGGGGGACTTTCGGGTCTGATGCTGCAGCTTATGCTAAGGAAGTCGAAGAACACATAACTTATG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 734

GAATCTCAGTATGGTTGCGCTCAGAAATGCATATCATGGCGGAAGTGCCGGTACGATTGGATTGACTGGTATGCAGACGTGGAAATACCCAATTCCTCAGgtatgtgtac ... atttttgcagGGTGAAATACATCATGTCATGAACCCTGATCCTTATCGGGGGACTTTCGGGTCTGATGCTGCAGCTTATGCTAAGGAAGTCGAAGAACACATAACTTATG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 571

GAATCTCAGTATGGTTGCGCTCAGAAATGCATATCATGGCGGAAGTGCCGGTACGATTGGATTGACTGGTATGCAGACGTGGAAATACCCAATTCCTCAGgtatgtgtac ... atttttgcagGGTGAAATACATCATGTCATGAACCCTGATCCTTATCGGGGGACTTTCGGGTCTGATGCTGCAGCTTATGCTAAGGAAGTCGAAGAACACATAACTTATG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aaaatgtatccatttctttattacatctatcatagcctcataagaatttttgcagGGTGAAATACATCATGTCATGAACCCTGATCCTTATCGGGGGACTTTCGGGTCTGATGCTGCAGCTTATGCTAAGGAAGTCGAAGAACACATAACTTATG
                                              tttttgc  CT-rich tract
           atttctttattacat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatgtgtacagtgtattgcgctttcatcaaattatttgactggttatgttttcaaagtcacatgtttgctgcagtagattcttagttatcaataattatctccgttctacccagcaaaaatgtatccatttctttattacatctatcatagcctcataagaatttttgcagGGTGAAATACATCATGTCATGAACCCTGATCCTTATCGGGGGACTTTCGGGTCTGATGCTGCAGCTTATGCTAAGGAAGTCGAAGAACACATAACTTATG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  ATGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGCAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAC