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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatgcttccgcgtgactctcatccaaacactatagaaaatgtggctgtccccttccatccctcgttatacgttcaaccaaacacacccttgtttggtctcccattttgccatggcatcaatgtagttatactatgtgagagttccctgttttgtagGCAATCGAGGAAACTGGCAGACGATTCAGAGACACTGTTCTTGCGCTTGGAGGTGGAAAGTCTCCGCTTGAG

Basic information

species Zea mays
transcript GRMZM2G133919_T01
intron # 15
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G133919_T01 (Zea mays), 3'ss of exon 15
lower sequence: LOC_Os02g58340.1 (Oryza sativa), 3'ss of exon 15
-----------------------------------------gtatgcttccgcgtgactctcatccaaacactatagaaaatgtggctgtccccttccatccctcgttatacgttcaaccaaacacacccttgtttggtc--tcccattttgccatggcatcaatgt-agttatactatgtgagagttccctgttttgtagGCAATCGAGGAAACTGGCAGACGATTCAGAGACACTGTTCTTGCGCTTGGAGGTGGAAAGTCTCCGCTTGAG
                                         | |||  ||    |||||    |   |    | |    ||  |   |      ||    |   |||   |  ||   ||  ||| | |  ||| |||    |   ||   |  | |  || ||  | | | ||| |   |     |      || | |||||||| |||||||||||||||||||||||||| || || |||||||||||||||||||| ||||| || |||
gtacagtttttcttgttttcccccatccagggaggtgctctggatgtgtcaaaatgacttgtttagtagtcattttcttaacttaatttgtttatttggccaaacgt---atattttgccctacaaaacaatgtgtggcacatagaatacagaaaggatataaaaatcaatgatattgactctagctatgactttatctagGCAATTGAGGAAACTGGCAGACGATTCAGAGAAACAGTCCTTGCGCTTGGAGGTGGAAAATCTCCACTCGAG
















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|32943210|gb|CF048029.1|CF048029
EST:     CAGCTGATGCATTCTCAGCTTTTGAAGACGCTGGTTTGGATGATGAGAAG                         GCAATCGAGGAAACTGGCAGACGATTCAGAGACACTGTTCTTGCGCTTGGA
genomic: CAGCTGATGCATTCTCAGCTTTTGAAGACGCTGGTTTGGATGATGAGAAGgtatgcttcc ... tgttttgtagGCAATCGAGGAAACTGGCAGACGATTCAGAGACACTGTTCTTGCGCTTGGA
EST: gi|14243309|gb|BG841007.2|BG841007
EST:     CAGCTGATGCATTCTCAGCTTTTGAAGACGCTGGTTTGGATGATGAGAAG                         GCAATCGAGGAAACTGGCAGACGATTCAGAGACACTGTTCTTGCGCTTGGA
genomic: CAGCTGATGCATTCTCAGCTTTTGAAGACGCTGGTTTGGATGATGAGAAGgtatgcttcc ... tgttttgtagGCAATCGAGGAAACTGGCAGACGATTCAGAGACACTGTTCTTGCGCTTGGA
EST: gi|5871243|gb|AW017714.1|AW017714
EST:     CAGCTGATGCATTCTCAGCTTTTGAAGACGCTGGTTTGGATGATGAGAAG                         GCAATCGAGGAAACTGGCAGACGATTCAGAGACACTGTTCTTGCGCTTGGA
genomic: CAGCTGATGCATTCTCAGCTTTTGAAGACGCTGGTTTGGATGATGAGAAGgtatgcttcc ... tgttttgtagGCAATCGAGGAAACTGGCAGACGATTCAGAGACACTGTTCTTGCGCTTGGA
EST: gi|40335046|gb|CK369116.1|CK369116
EST:     CAGCTGATGCATTCTCAGCTTTTGAAGACGCTGGTTTGGATGATGAGAAG                         GCAATCGAGGAAACTGGCAGACGATTCAGAGACACTGTTCTTGCGCTTGGA
genomic: CAGCTGATGCATTCTCAGCTTTTGAAGACGCTGGTTTGGATGATGAGAAGgtatgcttcc ... tgttttgtagGCAATCGAGGAAACTGGCAGACGATTCAGAGACACTGTTCTTGCGCTTGGA
EST: gi|116824661|gb|EC868295.1|EC868295
EST:     CAGCTGATGCATTCTCAGCTTTTGAAGACGCTGGTTTGGATGATGAGAAG                         GCAATCGAGGAAACTGGCAGACGATTCAGAGACACTGTTCTTGCGCTTGGA
genomic: CAGCTGATGCATTCTCAGCTTTTGAAGACGCTGGTTTGGATGATGAGAAGgtatgcttcc ... tgttttgtagGCAATCGAGGAAACTGGCAGACGATTCAGAGACACTGTTCTTGCGCTTGGA
EST: gi|14244905|gb|BG842843.2|BG842843
EST:     CAGCTGATGCATTCTCAGCTTTTGAAGACGCTGGTTTGGATGATGAGAAG                         GCAATCGAGGAAACTGGCAGACGATTCAGAGACACTGTTCTTGCGCTTGGA
genomic: CAGCTGATGCATTCTCAGCTTTTGAAGACGCTGGTTTGGATGATGAGAAGgtatgcttcc ... tgttttgtagGCAATCGAGGAAACTGGCAGACGATTCAGAGACACTGTTCTTGCGCTTGGA
EST: gi|6020894|gb|AW065822.1|AW065822
EST:     CAGCTGATGCATTCTCAGCTTTTGAAGACGCTGGTTTGGATGATGAGAAG                         GCAATCGAGGAAACTGGCAGACGATTCAGAGACACTGTTCTTGCGCTTGGA
genomic: CAGCTGATGCATTCTCAGCTTTTGAAGACGCTGGTTTGGATGATGAGAAGgtatgcttcc ... tgttttgtagGCAATCGAGGAAACTGGCAGACGATTCAGAGACACTGTTCTTGCGCTTGGA
EST: gi|485666|gb|T18736.1|T18736
EST:     CAGCTGATGCATNCTCAGCNTTTGAAGACGCTGGTTTGGATGATGAGAAG                         GCAATCGAGGAAACTGGCAGACGATTCAGAGACACTGTTCTTGCGCTTGGA
genomic: CAGCTGATGCATTCTCAGCTTTTGAAGACGCTGGTTTGGATGATGAGAAGgtatgcttcc ... tgttttgtagGCAATCGAGGAAACTGGCAGACGATTCAGAGACACTGTTCTTGCGCTTGGA
EST: gi|60401020|gb|DN233827.1|DN233827
EST:     CAGCTGATGCATTCTCAGCTTTTGAAGACGCTGGTTTGGATGATGAGAAG                         GCAATCGAGGAAACTGGCAGACGATTCAGAGACACTGTTCTTGCGCTTGGA
genomic: CAGCTGATGCATTCTCAGCTTTTGAAGACGCTGGTTTGGATGATGAGAAGgtatgcttcc ... tgttttgtagGCAATCGAGGAAACTGGCAGACGATTCAGAGACACTGTTCTTGCGCTTGGA
EST: gi|14242856|gb|BG840631.2|BG840631
EST:     CAGCTGATGCATTCTCAGCTTTTGAAGACGCTGGTTTGGATGATGAGAAG                         GCAATCGAGGAAACTGGCAGACGATTCAGAGACACTGTTCTTGCGCTTGGA
genomic: CAGCTGATGCATTCTCAGCTTTTGAAGACGCTGGTTTGGATGATGAGAAGgtatgcttcc ... tgttttgtagGCAATCGAGGAAACTGGCAGACGATTCAGAGACACTGTTCTTGCGCTTGGA
EST: gi|32909083|gb|CF013895.1|CF013895
EST:     CAGCTGATGCATTCTCAGCTTTTGAAGACGCTGGTTTGGATGATGAGAAG                         GCAATCGAGGAAACTGGCAGACGATTCAGAGACACTGTTCTTGCGCTTGGA
genomic: CAGCTGATGCATTCTCAGCTTTTGAAGACGCTGGTTTGGATGATGAGAAGgtatgcttcc ... tgttttgtagGCAATCGAGGAAACTGGCAGACGATTCAGAGACACTGTTCTTGCGCTTGGA
EST: gi|37382536|gb|CF628220.1|CF628220
EST:     CAGCTGATGCATTCTCAGCTTTTGAAGACGCTGGTTTGGATGATGAGAAG                         GCAATCGAGGAAACTGGCAGACGATTCAGAGACACTGTTCTTGCGCTTGGA
genomic: CAGCTGATGCATTCTCAGCTTTTGAAGACGCTGGTTTGGATGATGAGAAGgtatgcttcc ... tgttttgtagGCAATCGAGGAAACTGGCAGACGATTCAGAGACACTGTTCTTGCGCTTGGA
EST: gi|31997605|gb|CD661676.1|CD661676
EST:     CAGCTGATGCATTCTCAGCTTTTGAAGACGCTGGTTTGGATGATGAGAAG                         GCAATCGAGGAAACTGGCAGACGATTCAGAGACACTGTTCTTGCGCTTGGA
genomic: CAGCTGATGCATTCTCAGCTTTTGAAGACGCTGGTTTGGATGATGAGAAGgtatgcttcc ... tgttttgtagGCAATCGAGGAAACTGGCAGACGATTCAGAGACACTGTTCTTGCGCTTGGA
EST: gi|78021291|gb|DV489678.1|DV489678
EST:     CAGCTGATGCATTCTCAGCTTTTGAAGACGCTGGTTTGGATGATGAGAAG                         GCAATCGAGGAAACTGGCAGACGATTCAGAGACACTGTTCTTGCGCTTGGA
genomic: CAGCTGATGCATTCTCAGCTTTTGAAGACGCTGGTTTGGATGATGAGAAGgtatgcttcc ... tgttttgtagGCAATCGAGGAAACTGGCAGACGATTCAGAGACACTGTTCTTGCGCTTGGA
EST: gi|40336438|gb|CK370508.1|CK370508
EST:     CTGCTGATGCATTCTCAGCTTTTGAAGACGCTGGTTTGGATGATGAGAAG                         GCAATCGAGGAAACTGGCAGACGATTCAGAGACACTGTTCTTGCGCTTGGA
genomic: CAGCTGATGCATTCTCAGCTTTTGAAGACGCTGGTTTGGATGATGAGAAGgtatgcttcc ... tgttttgtagGCAATCGAGGAAACTGGCAGACGATTCAGAGACACTGTTCTTGCGCTTGGA
EST: gi|149075397|gb|EE163911.2|EE163911
EST:     CAGCTGATGCATTCTCAGCTTTTGAAGACGCTGGTTTGGATGATGAGAAG                         GCAATCGAGGAAACTGGCAGACGATTCAGAGACACTGTTCTTGCGCTTGGA
genomic: CAGCTGATGCATTCTCAGCTTTTGAAGACGCTGGTTTGGATGATGAGAAGgtatgcttcc ... tgttttgtagGCAATCGAGGAAACTGGCAGACGATTCAGAGACACTGTTCTTGCGCTTGGA
EST: gi|33097696|gb|CF057656.1|CF057656
EST:     CAGCTGATGCATTCTCAGCTTTTGAAGACGCTGGTTTGGATGATGAGAAG                         GCAATCGAGGAAACTGGCAGACGATTCAGAGACACTGTTCTTGCGCTTGGA
genomic: CAGCTGATGCATTCTCAGCTTTTGAAGACGCTGGTTTGGATGATGAGAAGgtatgcttcc ... tgttttgtagGCAATCGAGGAAACTGGCAGACGATTCAGAGACACTGTTCTTGCGCTTGGA
EST: gi|28982897|gb|BQ538418.2|BQ538418
EST:     CAGCTGATGCATTCTCAGCTTTTGAAGACGCTGGTTTGGATGATGAGAAG                         GCAATCGAGGAAACTGGCAGACGATTCAGAGACACTGTTCTTGCGCTTGGA
genomic: CAGCTGATGCATTCTCAGCTTTTGAAGACGCTGGTTTGGATGATGAGAAGgtatgcttcc ... tgttttgtagGCAATCGAGGAAACTGGCAGACGATTCAGAGACACTGTTCTTGCGCTTGGA
EST: gi|29543522|gb|CB603904.1|CB603904
EST:     CAGCTGATGCATTCTCAGCTTTTGAAGACGCTGGTTTGGATGATGAGAAG                         GCAATCGAGGAAACTGGCAGACGATTCAGAGACACTGTTCTTGCGCTTGGA
genomic: CAGCTGATGCATTCTCAGCTTTTGAAGACGCTGGTTTGGATGATGAGAAGgtatgcttcc ... tgttttgtagGCAATCGAGGAAACTGGCAGACGATTCAGAGACACTGTTCTTGCGCTTGGA
EST: gi|149009255|gb|EE153869.2|EE153869
EST:     CAGCTGATGCATTTTCAGCTTTTGAAGACGCTGGTTTGGATGATGAGAAG                         GCAATCGAGGAAACTGGCAGACGATTCAGAGACACTGTTCTTGCGCTTGGA
genomic: CAGCTGATGCATTCTCAGCTTTTGAAGACGCTGGTTTGGATGATGAGAAGgtatgcttcc ... tgttttgtagGCAATCGAGGAAACTGGCAGACGATTCAGAGACACTGTTCTTGCGCTTGGA
EST: gi|14244353|gb|BG842414.2|BG842414
EST:     CAGCTGATGCATTCTCAGCTTTTGAAGACGCTGGTTTGGATGATGAGAAG                         GCAATCGAGGAAACTGGCAGACGATTCAGAGACACTGTTCTTGCGCTTGGA
genomic: CAGCTGATGCATTCTCAGCTTTTGAAGACGCTGGTTTGGATGATGAGAAGgtatgcttcc ... tgttttgtagGCAATCGAGGAAACTGGCAGACGATTCAGAGACACTGTTCTTGCGCTTGGA
EST: gi|40335258|gb|CK369328.1|CK369328
EST:     CAGCTGATGCATTCTCAGCTTTTGAAGACGCTGGTTTGGATGATGAGAAG                         GCAATCGAGGAAACTGGCAGACGATTCAGAGACACTGTTCTTGCGCTTGGA
genomic: CAGCTGATGCATTCTCAGCTTTTGAAGACGCTGGTTTGGATGATGAGAAGgtatgcttcc ... tgttttgtagGCAATCGAGGAAACTGGCAGACGATTCAGAGACACTGTTCTTGCGCTTGGA
EST: gi|15589996|gb|BI674612.1|BI674612
EST:     CAGCTGATGCATTCTCAGCTTTTGAAGACGCTGGTTTGGATGATGAGAAG                         GCAATCGAGGAAACTGGCAGACGATTCAGAGACACTGTTCTTGCGCTTGGA
genomic: CAGCTGATGCATTCTCAGCTTTTGAAGACGCTGGTTTGGATGATGAGAAGgtatgcttcc ... tgttttgtagGCAATCGAGGAAACTGGCAGACGATTCAGAGACACTGTTCTTGCGCTTGGA
EST: gi|71758760|gb|DR956697.1|DR956697
EST:     CAGCTGATGCATTCTCAGCTTTTGAAGACGCTGGTTTGGATGATGAGAAG                         GCAATCGAGGAAACTGGCAGACGATTCAGAGACACTGTTCTTGCGCTGGGA
genomic: CAGCTGATGCATTCTCAGCTTTTGAAGACGCTGGTTTGGATGATGAGAAGgtatgcttcc ... tgttttgtagGCAATCGAGGAAACTGGCAGACGATTCAGAGACACTGTTCTTGCGCTTGGA
EST: gi|67022921|gb|CO451670.1|CO451670
EST:     CAGCTGATGCATTCTCAGCTTTTGAAGACGCTGGTTTGGATGATGAGAAG                         GCAATCGAGGAAACTGGCAGACGATTCAGAGACACTGTTCTTGCGCTTGGA
genomic: CAGCTGATGCATTCTCAGCTTTTGAAGACGCTGGTTTGGATGATGAGAAGgtatgcttcc ... tgttttgtagGCAATCGAGGAAACTGGCAGACGATTCAGAGACACTGTTCTTGCGCTTGGA
EST: gi|110220920|gb|EC902818.1|EC902818
EST:     CAGCTGATGCATTTTCAGCTTTTGAAGACGCTGGTTTGGATGATGAGAAG                         GCAATCGAGGAAACTGGCAGACGATTCAGAGACACTGTTCTTGCGCTTGGA
genomic: CAGCTGATGCATTCTCAGCTTTTGAAGACGCTGGTTTGGATGATGAGAAGgtatgcttcc ... tgttttgtagGCAATCGAGGAAACTGGCAGACGATTCAGAGACACTGTTCTTGCGCTTGGA
EST: gi|32843192|gb|CD982873.1|CD982873
EST:     CAGCTGATGCATTCTCAGCTTTTGAAGACGCTGGTTTGGATGATGAGAAG                         GCAATCGAGGAAACTGGCAGACGATTCAGGGACACTGTTCTTGCGCTTGGA
genomic: CAGCTGATGCATTCTCAGCTTTTGAAGACGCTGGTTTGGATGATGAGAAGgtatgcttcc ... tgttttgtagGCAATCGAGGAAACTGGCAGACGATTCAGAGACACTGTTCTTGCGCTTGGA

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: 120

TGGGCTGAAGTACTGTCAGCTGATGCATTCTCAGCTTTTGAAGACGCTGGTTTGGATGATGAGAAGgtatgcttcc ... tgttttgtagGCAATCGAGGAAACTGGCAGACGATTCAGAGACACTGTTCTTGCGCTTGGAGGTGGAAAGTCTCCGCTTGAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 128

TGGGCTGAAGTACTGTCAGCTGATGCATTCTCAGCTTTTGAAGACGCTGGTTTGGATGATGAGAAGgtatgcttcc ... tgttttgtagGCAATCGAGGAAACTGGCAGACGATTCAGAGACACTGTTCTTGCGCTTGGAGGTGGAAAGTCTCCGCTTGAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 93

TGGGCTGAAGTACTGTCAGCTGATGCATTCTCAGCTTTTGAAGACGCTGGTTTGGATGATGAGAAGgtatgcttcc ... tgttttgtagGCAATCGAGGAAACTGGCAGACGATTCAGAGACACTGTTCTTGCGCTTGGAGGTGGAAAGTCTCCGCTTGAG


Block sizes: 48 (upstream exon), 47 (downstream exon)
Score: 124

TGGGCTGAAGTACTGTCAGCTGATGCATTCTCAGCTTTTGAAGACGCTGGTTTGGATGATGAGAAGgtatgcttcc ... tgttttgtagGCAATCGAGGAAACTGGCAGACGATTCAGAGACACTGTTCTTGCGCTTGGAGGTGGAAAGTCTCCGCTTGAG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cattttgccatggcatcaatgtagttatactatgtgagagttccctgttttgtagGCAATCGAGGAAACTGGCAGACGATTCAGAGACACTGTTCTTGCGCTTGGAGGTGGAAAGTCTCCGCTTGAG
                                        ttccctgtttt  CT-rich tract
                        ttatactat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatgcttccgcgtgactctcatccaaacactatagaaaatgtggctgtccccttccatccctcgttatacgttcaaccaaacacacccttgtttggtctcccattttgccatggcatcaatgtagttatactatgtgagagttccctgttttgtagGCAATCGAGGAAACTGGCAGACGATTCAGAGACACTGTTCTTGCGCTTGGAGGTGGAAAGTCTCCGCTTGAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGTGGA