Skip to another splice site:
1  
 5'  3'   		2  
 5'  3'   		3  
 5'  3'   		4  
 5'  3'   		5  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagttgttttcaacatcttcttttctttttatattcccaccccaagcatgttagtattccatgtgcatgttctaaaccctaaagctatggatgctatccggaaaacagGTTAGCGAGCGGGAAGACAAGCTATTCCTCGACCAGATTGATTCCCTAATGGAACAAAACGCAGAGGTCGATGGTGACGTGGACAGTGAAGAGGAGGAAG

Basic information

species Zea mays
transcript GRMZM2G058138_T01
intron # 4
splice site 3'
intron type U2

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|5058755|gb|AI737231.1|AI737231
EST:     AGATTGAAAAATACAAAGGAAAGTTAGTAGTGAAGGAACCACCAAGAGCT                         GTTAGCGAGCGGGAAGACAAGCTATTCCTCGACCAGATTGATTCCCTAATG
genomic: AGATTGAAAAATACAAAGGAAAGTTAGTAGTGAAGGAACCACCAAGAGCTgtaagttgtt ... cggaaaacagGTTAGCGAGCGGGAAGACAAGCTATTCCTCGACCAGATTGATTCCCTAATG
EST: gi|60349894|gb|DN216867.1|DN216867
EST:     AGATTGAAAAATACAAAGGAAAGTTAGTAGTGAAGGAACCACCAAGAGCT                         GTTAGCGAGCGGGAAGACAAGCTATTCCTCGACCAGATTGATTCCCTAATG
genomic: AGATTGAAAAATACAAAGGAAAGTTAGTAGTGAAGGAACCACCAAGAGCTgtaagttgtt ... cggaaaacagGTTAGCGAGCGGGAAGACAAGCTATTCCTCGACCAGATTGATTCCCTAATG
EST: gi|61117523|gb|DN558484.1|DN558484
EST:     AGATTGAAAAATACAAAGGAAAGTTAGTAGTGAAGGAACCACCAAGAGCT                         GTTAGCGAGCGGGAAGACAAGCTATTCCTCGACCAGATTGATTCCCTAATG
genomic: AGATTGAAAAATACAAAGGAAAGTTAGTAGTGAAGGAACCACCAAGAGCTgtaagttgtt ... cggaaaacagGTTAGCGAGCGGGAAGACAAGCTATTCCTCGACCAGATTGATTCCCTAATG
EST: gi|31406196|gb|CD484928.1|CD484928
EST:     AGATTGAAAAATACAAAGGAAAGTTAGTAGTGAAGGAACCACCAAGAGCT                         GTTAGCGAGCGGGAAGACAAGCTATTCCTCGACCAGATTGATTCCCTAATG
genomic: AGATTGAAAAATACAAAGGAAAGTTAGTAGTGAAGGAACCACCAAGAGCTgtaagttgtt ... cggaaaacagGTTAGCGAGCGGGAAGACAAGCTATTCCTCGACCAGATTGATTCCCTAATG
EST: gi|13490893|gb|BG517657.1|BG517657
EST:     AGATTGAAAAATACAAAGGAAAGTTAGTAGTGAAGGAACCACCAAGAGCT                         GTTAGCGAGCGGGAAGACAAGCTATTCCTCGACCAGATTGATTCCCTAATG
genomic: AGATTGAAAAATACAAAGGAAAGTTAGTAGTGAAGGAACCACCAAGAGCTgtaagttgtt ... cggaaaacagGTTAGCGAGCGGGAAGACAAGCTATTCCTCGACCAGATTGATTCCCTAATG
EST: gi|9731744|gb|BE510496.1|BE510496
EST:     AGATTGAAAAATACAAAGGAAAGTTAGTAGTGAAGGAACCACCAAGAGCT                         GTTAGCGAGCGGGAAGACAAGCTATTCCTCGACCAGATTGATTCCCTAATG
genomic: AGATTGAAAAATACAAAGGAAAGTTAGTAGTGAAGGAACCACCAAGAGCTgtaagttgtt ... cggaaaacagGTTAGCGAGCGGGAAGACAAGCTATTCCTCGACCAGATTGATTCCCTAATG
EST: gi|87152809|gb|DY397598.1|DY397598
EST:     AGATTGAAAAATACAAAGGAAAGTTAGTAGTGAAGGAACCACCAAGAGCT                         GTTAGCGAGCGGGAAGACAAGCTATTCCTCGACCAGATTGATTCCCTAATG
genomic: AGATTGAAAAATACAAAGGAAAGTTAGTAGTGAAGGAACCACCAAGAGCTgtaagttgtt ... cggaaaacagGTTAGCGAGCGGGAAGACAAGCTATTCCTCGACCAGATTGATTCCCTAATG
EST: gi|4804424|gb|AI665225.2|AI665225
EST:     AGATTGAAAAATACAAAGGAAAGTTAGTAGTGAAGGAACCACCAAGAGCT                         GTTAGCGAGCGGGAAGACAAGCTATTCCTCGACCAGATTGATTCCCTAATG
genomic: AGATTGAAAAATACAAAGGAAAGTTAGTAGTGAAGGAACCACCAAGAGCTgtaagttgtt ... cggaaaacagGTTAGCGAGCGGGAAGACAAGCTATTCCTCGACCAGATTGATTCCCTAATG
EST: gi|61117524|gb|DN558485.1|DN558485
EST:     AGATTGAAAAATACAAAGGAAAGTTAGTAGTGAAGGAACCACCAAGAGCT                         GTTAGCGAGCGGGAAGACAAGCTATTCCTCGACCAGATTGATTCCCTAATG
genomic: AGATTGAAAAATACAAAGGAAAGTTAGTAGTGAAGGAACCACCAAGAGCTgtaagttgtt ... cggaaaacagGTTAGCGAGCGGGAAGACAAGCTATTCCTCGACCAGATTGATTCCCTAATG
EST: gi|5108096|gb|AI739809.1|AI739809
EST:     AGATTGAAAAATACAAAGGAAAGTTAGTAGTGAAGGAACCACCAAGAGCT                         GTTAGCGAGCGGGAAGACAAGCTATTCCTCGACCAGATTGATTCCCTAATG
genomic: AGATTGAAAAATACAAAGGAAAGTTAGTAGTGAAGGAACCACCAAGAGCTgtaagttgtt ... cggaaaacagGTTAGCGAGCGGGAAGACAAGCTATTCCTCGACCAGATTGATTCCCTAATG
EST: gi|84977363|gb|DW475785.1|DW475785
EST:     AGATTGAAAAATACAAAGGAAAGTTAGTAGTGAAGGAACCACCAAGAGCT                         GTTAGCGAGCGGGAAGACAAGCTATTCCTCGACCAGATTGATTCCCTAATG
genomic: AGATTGAAAAATACAAAGGAAAGTTAGTAGTGAAGGAACCACCAAGAGCTgtaagttgtt ... cggaaaacagGTTAGCGAGCGGGAAGACAAGCTATTCCTCGACCAGATTGATTCCCTAATG
EST: gi|19436423|gb|BM952833.1|BM952833
EST:     AGATTGAAAAATACAAAGGAAAGTTAGTAGTGAAGGAACCACCAAGAGCT                         GTTAGCGAGCGGGAAGACAAGCTATTCCTCGACCAGATTGATTCCCTAATG
genomic: AGATTGAAAAATACAAAGGAAAGTTAGTAGTGAAGGAACCACCAAGAGCTgtaagttgtt ... cggaaaacagGTTAGCGAGCGGGAAGACAAGCTATTCCTCGACCAGATTGATTCCCTAATG
EST: gi|13491041|gb|BG517805.1|BG517805
EST:     AGATTGAAAAATACAAAGGAAAGTTAGTAGTGAAGGAACCACCAAGAGCT                         GTTAGCGAGCGGGAAGACAAGCTATTCCTCGACCAG
genomic: AGATTGAAAAATACAAAGGAAAGTTAGTAGTGAAGGAACCACCAAGAGCTgtaagttgtt ... cggaaaacagGTTAGCGAGCGGGAAGACAAGCTATTCCTCGACCAG
EST: gi|76292257|gb|DV031825.1|DV031825
EST:     AGATTGAAAAATACAAAGGAAAGTTAGTAGTGAAGGAACCACCAAGAGCT                         GTTAGCGAGCGGGAAGACAAGCTATTCCTCGACCAGATTGATTCCCTAATG
genomic: AGATTGAAAAATACAAAGGAAAGTTAGTAGTGAAGGAACCACCAAGAGCTgtaagttgtt ... cggaaaacagGTTAGCGAGCGGGAAGACAAGCTATTCCTCGACCAGATTGATTCCCTAATG
EST: gi|15632489|gb|BI679582.1|BI679582
EST:     AGATTGAAAAATACAAAGGAAAGTTAGTAGTGAAGGAACCACCAAGAGCT                         GTTAGCGAGCGGGAAGACAAGCTATTCCTCGACCAGATTGATTCCCTAATG
genomic: AGATTGAAAAATACAAAGGAAAGTTAGTAGTGAAGGAACCACCAAGAGCTgtaagttgtt ... cggaaaacagGTTAGCGAGCGGGAAGACAAGCTATTCCTCGACCAGATTGATTCCCTAATG
EST: gi|4776664|gb|AI665667.1|AI665667
EST:     AGATTGAAAAATACAAAGGAAAGTTAGTAGTGAAGGAACCACCAAGAGCT                         GTTAGCGAGCGGGAAGCCAAGCTATTCCTCGACCAGATTGATTCCCTAATG
genomic: AGATTGAAAAATACAAAGGAAAGTTAGTAGTGAAGGAACCACCAAGAGCTgtaagttgtt ... cggaaaacagGTTAGCGAGCGGGAAGACAAGCTATTCCTCGACCAGATTGATTCCCTAATG
EST: gi|61117522|gb|DN558483.1|DN558483
EST:     AGATTGAAAAATACAAAGGAAAGTTAGTAGTGAAGGAACCACCAAGAGCT                         GTTAGCGAGCGGGAAGACAAGCTATTCCTCGACCAGATTGATTCCCTAATG
genomic: AGATTGAAAAATACAAAGGAAAGTTAGTAGTGAAGGAACCACCAAGAGCTgtaagttgtt ... cggaaaacagGTTAGCGAGCGGGAAGACAAGCTATTCCTCGACCAGATTGATTCCCTAATG
EST: gi|32930323|gb|CF035135.1|CF035135
EST:     AGATTGAAAAATACAAAGGAAAGTTAGTAGTGAAGGAACCACCAAGAGCT                         GTTAGCGAGCGGGAAGACAAGCTATTCCTCGACCAGATTGATTCCCTAATG
genomic: AGATTGAAAAATACAAAGGAAAGTTAGTAGTGAAGGAACCACCAAGAGCTgtaagttgtt ... cggaaaacagGTTAGCGAGCGGGAAGACAAGCTATTCCTCGACCAGATTGATTCCCTAATG
EST: gi|12969140|gb|BG266085.1|BG266085
EST:     AGATTGAAAAATACAAAGGAAAGTTAGTAGTGAAGGAACCACCAAGAGCT                         GTTAGCGAGCGGGAAGACAAGCTATTCCTCGACCAGATTGATTCCCTAATG
genomic: AGATTGAAAAATACAAAGGAAAGTTAGTAGTGAAGGAACCACCAAGAGCTgtaagttgtt ... cggaaaacagGTTAGCGAGCGGGAAGACAAGCTATTCCTCGACCAGATTGATTCCCTAATG
EST: gi|29576855|gb|CB616967.1|CB616967
EST:     AGATTGAAAAATAAAAAGGAAAGTTAGTAGTGAAGGAACCGCCAAGAGCT                         GTTAGCGAGCGGGAAGACAAGCTATTCCTCGACCAGATTGATTCCCTAATG
genomic: AGATTGAAAAATACAAAGGAAAGTTAGTAGTGAAGGAACCACCAAGAGCTgtaagttgtt ... cggaaaacagGTTAGCGAGCGGGAAGACAAGCTATTCCTCGACCAGATTGATTCCCTAATG
EST: gi|61117520|gb|DN558481.1|DN558481
EST:     AGATTGAAAAATACAAAGGAAAGTTAGTAGTGAAGGAACCACCAAGAGCT                         GTTAGCGAGCGGGAAGACAAGCTATTCCTCGACCAGATTGATTCCCTAATG
genomic: AGATTGAAAAATACAAAGGAAAGTTAGTAGTGAAGGAACCACCAAGAGCTgtaagttgtt ... cggaaaacagGTTAGCGAGCGGGAAGACAAGCTATTCCTCGACCAGATTGATTCCCTAATG
EST: gi|6721022|gb|AW308659.1|AW308659
EST:     AGATTGAAAAATACAAAGGAAAGTTAGTAGTGAAGGAACCACCAAGAGCT                         GTTAGCGAGCGGGAAGACAAGCTATTCCTCGACCAGATTGATTCCCTAATG
genomic: AGATTGAAAAATACAAAGGAAAGTTAGTAGTGAAGGAACCACCAAGAGCTgtaagttgtt ... cggaaaacagGTTAGCGAGCGGGAAGACAAGCTATTCCTCGACCAGATTGATTCCCTAATG
EST: gi|22491009|gb|BU050932.1|BU050932
EST:     AGATTGAAAAATACAAAGGAAAGTTAGTAGTGAAGGAACCACCAAGAGCT                         GTTAGCGAGCGGGAAGACAAGCTATTCCTCGACCAGATTGATTCCCTAATG
genomic: AGATTGAAAAATACAAAGGAAAGTTAGTAGTGAAGGAACCACCAAGAGCTgtaagttgtt ... cggaaaacagGTTAGCGAGCGGGAAGACAAGCTATTCCTCGACCAGATTGATTCCCTAATG
EST: gi|8665269|gb|BE186085.1|BE186085
EST:     GATTGTAAAAATACAAAGGAAAGTTAGTAGTGAAGGAACCCCCAAGAGCT                         GTTAGCGAGCGGGAAGACAAGCTATTCCTCGACCAGATTGATTCCCTAATG
genomic: GATTG-AAAAATACAAAGGAAAGTTAGTAGTGAAGGAACCACCAAGAGCTgtaagttgtt ... cggaaaacagGTTAGCGAGCGGGAAGACAAGCTATTCCTCGACCAGATTGATTCCCTAATG
EST: gi|19436422|gb|BM952832.1|BM952832
EST:     AGATTGAAAAATACAAAGGAAAGTTAGTAGTGAAGGAACCACCAAGAGCT                         GTTAGCGAGCGGGAAGACAAGCTATTCCTCGACCAGATTGATTCCCTAATG
genomic: AGATTGAAAAATACAAAGGAAAGTTAGTAGTGAAGGAACCACCAAGAGCTgtaagttgtt ... cggaaaacagGTTAGCGAGCGGGAAGACAAGCTATTCCTCGACCAGATTGATTCCCTAATG
EST: gi|26557327|gb|CA829562.1|CA829562
EST:     AGATTGAAAAATACAAAGGAAAGTTAGTAGTGAAGGAACCCCCAAGAGCT                         GTTAGCGAGCGGGAAGACAAGCTATTCCTCGACCAGATTGATTCCCTAATG
genomic: AGATTGAAAAATACAAAGGAAAGTTAGTAGTGAAGGAACCACCAAGAGCTgtaagttgtt ... cggaaaacagGTTAGCGAGCGGGAAGACAAGCTATTCCTCGACCAGATTGATTCCCTAATG
EST: gi|32931662|gb|CF036474.1|CF036474
EST:     AGATTGAAAAATACAAAGGAAAGTTAGTAGTGAAGGAACCACCAAGAGCT                         GTTAGCGAGCGGGAAGACAAGCTATTCCTCGACCAGATTGATTCCCTAATG
genomic: AGATTGAAAAATACAAAGGAAAGTTAGTAGTGAAGGAACCACCAAGAGCTgtaagttgtt ... cggaaaacagGTTAGCGAGCGGGAAGACAAGCTATTCCTCGACCAGATTGATTCCCTAATG

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: 47 (upstream exon), 47 (downstream exon)
Score: 201

GACCAAGGGATTTCAGTTCTCACTGATGCAGTCAAGGCTTGTACAGCAGAGATTGAAAAATACAAAGGAAAGTTAGTAGTGAAGGAACCACCAAGAGCTgtaagttgtt ... cggaaaacagGTTAGCGAGCGGGAAGACAAGCTATTCCTCGACCAGATTGATTCCCTAATGGAACAAAACGCAGAGGTCGATGGTGACGTGGACAGTGAAGAGGAGGAAG


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 213

GACCAAGGGATTTCAGTTCTCACTGATGCAGTCAAGGCTTGTACAGCAGAGATTGAAAAATACAAAGGAAAGTTAGTAGTGAAGGAACCACCAAGAGCTgtaagttgtt ... cggaaaacagGTTAGCGAGCGGGAAGACAAGCTATTCCTCGACCAGATTGATTCCCTAATGGAACAAAACGCAGAGGTCGATGGTGACGTGGACAGTGAAGAGGAGGAAG


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 189

GACCAAGGGATTTCAGTTCTCACTGATGCAGTCAAGGCTTGTACAGCAGAGATTGAAAAATACAAAGGAAAGTTAGTAGTGAAGGAACCACCAAGAGCTgtaagttgtt ... cggaaaacagGTTAGCGAGCGGGAAGACAAGCTATTCCTCGACCAGATTGATTCCCTAATGGAACAAAACGCAGAGGTCGATGGTGACGTGGACAGTGAAGAGGAGGAAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 203

GACCAAGGGATTTCAGTTCTCACTGATGCAGTCAAGGCTTGTACAGCAGAGATTGAAAAATACAAAGGAAAGTTAGTAGTGAAGGAACCACCAAGAGCTgtaagttgtt ... cggaaaacagGTTAGCGAGCGGGAAGACAAGCTATTCCTCGACCAGATTGATTCCCTAATGGAACAAAACGCAGAGGTCGATGGTGACGTGGACAGTGAAGAGGAGGAAG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gtattccatgtgcatgttctaaaccctaaagctatggatgctatccggaaaacagGTTAGCGAGCGGGAAGACAAGCTATTCCTCGACCAGATTGATTCCCTAATGGAACAAAACGCAGAGGTCGATGGTGACGTGGACAGTGAAGAGGAGGAAG
                ttctaaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaagttgttttcaacatcttcttttctttttatattcccaccccaagcatgttagtattccatgtgcatgttctaaaccctaaagctatggatgctatccggaaaacagGTTAGCGAGCGGGAAGACAAGCTATTCCTCGACCAGATTGATTCCCTAATGGAACAAAACGCAGAGGTCGATGGTGACGTGGACAGTGAAGAGGAGGAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGGA