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

...tgaatgttagtaacactaacacctagggttaaggtgggcttgcttgctacatcttgtcttttcactttgacagtaggtaatcggatattacttgttacagGTGGACCGTGTTCTTTATTCCTCTGTTGTTTACCCACATAACTATGGCTTCATTCCACGCACACTCTGTGAGGATAACGACCCCCTGGATGTCCTCATAC

Basic information

species Zea mays
transcript GRMZM2G046587_T03
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G046587_T03 (Zea mays), 3'ss of exon 1
lower sequence: LOC_Os02g47600.2 (Oryza sativa), 3'ss of exon 4
tgaatgttagtaacactaacacctagggttaag-gtgggcttgcttgctacatcttgtcttttcactttgacagtaggtaatc---ggatattacttgt--tacagGTGGACCGTGTTCTTTATTCCTCTGTTGTTTACCCACATAACTATGGCTTCATTCCACGCACACTCTGTGAGGATAACGACCCCCTGGATGTCCTCATAC
       ||| |    ||    |  || | | | | |||  |||     ||  ||| | |||  || ||||||  ||  ||       || |||| |||  | ||||| || ||||||||||| || ||||||||||||||||| |||||||| ||||||||||||||||| ||||||||    |||||| |||| |||||| | |
-----agtaggatggttagtgacagggataatgcgaggggctgcaataaacgacttat-tttcaacattgacaaaagagaacttgaaaattttacctgtgtttcagGTTGATCGTGTTCTTTACTCATCTGTTGTTTACCCACACAACTATGGTTTCATTCCACGCACACTTTGTGAGGACGGTGACCCCATGGACGTCCTCGTCC

upper sequence: GRMZM2G046587_T03 (Zea mays), 3'ss of exon 1
lower sequence: Vv04s0023g02050.t01 (Vitis vinifera), 3'ss of exon 3
tgaatgttagtaacactaacacc-tagggttaaggtgggcttgcttgctacatcttgtcttttcactttgacagtaggtaatcggatattacttgttacagGTGGACCGTGTTCTTTATTCCTCTGTTGTTTACCCACATAACTATGGCTTCATTCCACGCACACTCTGTGAGGATAACGACCCCCTGGATGTCCTCATAC
|   || |  ||   ||   |   |   | ||   |     || ||  |  ||    ||  |  | |  || ||      |  |||  |  |     | |||| || ||||||||||| || || |||||||| |||||||||||||| ||||| || || ||  ||||||| || | ||| ||  |||||||||| || |
tttttgcttatattgctgttatagtgttgctagattatatctgatttgtgtatgcactcaatata-taagatagctaaagaatggagttctccaaaaatagGTTGATCGTGTTCTTTACTCATCAGTTGTTTATCCACATAACTATGGTTTCATCCCTCGAACCATCTGTGAAGACAGCGATCCTATGGATGTCCTGATTC
















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|19351061|gb|BM895593.1|BM895593
EST:     AAGTACGAGTTGGACAAGGCATCTGGTCTGATCAAG                         GTGGACCGTGTTCTTTATTCCTCTGTTGTTTACCCACATAACTATGGCTTC
genomic: AAGTACGAGTTGGACAAGGCATCTGGTCTGATCAAGgtgagatcca ... cttgttacagGTGGACCGTGTTCTTTATTCCTCTGTTGTTTACCCACATAACTATGGCTTC
EST: gi|32849179|gb|CD988860.1|CD988860
EST:     ACGAGTTGGACAAGGCATCTGGTCTGATCAAG                         GTGGACCGTGTTCTTTATTCCTCTGTTGTTTACCCACATAACTATGGCTTC
genomic: ACGAGTTGGACAAGGCATCTGGTCTGATCAAGgtgagatcca ... cttgttacagGTGGACCGTGTTCTTTATTCCTCTGTTGTTTACCCACATAACTATGGCTTC
EST: gi|32924525|gb|CF029337.1|CF029337
EST:     ACGAGTTGGACAAGGCATCTGGTCTGATCAAG                         GTGGACCGTGTTCTTTATTCCTCTGTTGTTTACCCACATAACTATGGCTTC
genomic: ACGAGTTGGACAAGGCATCTGGTCTGATCAAGgtgagatcca ... cttgttacagGTGGACCGTGTTCTTTATTCCTCTGTTGTTTACCCACATAACTATGGCTTC
EST: gi|18168735|gb|BM338575.1|BM338575
EST:     GGTCTGATCAAG                         GTGGACCGTGTTCTTTATTCCTCTGTTGTTTACCCACATAACTATGGCTTC
genomic: GGTCTGATCAAGgtgagatcca ... cttgttacagGTGGACCGTGTTCTTTATTCCTCTGTTGTTTACCCACATAACTATGGCTTC
EST: gi|60348368|gb|DN215341.1|DN215341
EST:     GAGGCAGCAAGGTTAAGTACGAGTTGGACAAGGCATCTGGTCTGATCAAG                         GTGGACCGTGTTCTTTATTCCTCTGTTGTTTACCCACATAACTATGGCTTC
genomic: GAGGCAGCAAGGTTAAGTACGAGTTGGACAAGGCATCTGGTCTGATCAAGgtgagatcca ... cttgttacagGTGGACCGTGTTCTTTATTCCTCTGTTGTTTACCCACATAACTATGGCTTC
EST: gi|149099848|gb|EE185900.2|EE185900
EST:     GGCAGCAAGGTTAAGTACGAGTTGGACAAGGCATCTGGTTTGATCAAG                         GTGGACCGTGTTCTTTATTCCTCTGTTGTTTACCCACATAACTATGGCTTC
genomic: GGCAGCAAGGTTAAGTACGAGTTGGACAAGGCATCTGGTCTGATCAAGgtgagatcca ... cttgttacagGTGGACCGTGTTCTTTATTCCTCTGTTGTTTACCCACATAACTATGGCTTC
EST: gi|17931649|gb|BM268609.1|BM268609
EST:     GAGGCAGCAAGGTTAAGTACGAGTTGGACAAGGCATCTGGTCTGATCAAG                         GTGGACCGTGTTCTTTATTCCTCTGTTGTTTACCCACATAACTATGGCTTC
genomic: GAGGCAGCAAGGTTAAGTACGAGTTGGACAAGGCATCTGGTCTGATCAAGgtgagatcca ... cttgttacagGTGGACCGTGTTCTTTATTCCTCTGTTGTTTACCCACATAACTATGGCTTC
EST: gi|74244614|gb|DT652528.1|DT652528
EST:     GAGGCAGCAAGGTTAAGTACGAGTTGGACAAGGCATCTGGTCTGATCAAG                         GTGGACCGTGTTCTTTATTCCTCTGTTGTTTACCCACATAACTATGGCTTC
genomic: GAGGCAGCAAGGTTAAGTACGAGTTGGACAAGGCATCTGGTCTGATCAAGgtgagatcca ... cttgttacagGTGGACCGTGTTCTTTATTCCTCTGTTGTTTACCCACATAACTATGGCTTC
EST: gi|32924252|gb|CF029064.1|CF029064
EST:     ACGAGTTGGACAAGGCATCTGGTCTGATCAAG                         GTGGACCGTGTTCTTTATTCCTCTGTTGTTTACCCACATAACTATGGCTTC
genomic: ACGAGTTGGACAAGGCATCTGGTCTGATCAAGgtgagatcca ... cttgttacagGTGGACCGTGTTCTTTATTCCTCTGTTGTTTACCCACATAACTATGGCTTC
EST: gi|32831285|gb|CD970963.1|CD970963
EST:     AGTTGGACAAGGCATCTGGTCTGATCAAG                         GTGGACCGTG-TCTNTTATCCCTCTGTTGTTTACCCACATAACTATGGCTT
genomic: AGTTGGACAAGGCATCTGGTCTGATCAAGgtgagatcca ... cttgttacagGTGGACCGTGTTCT-TTATTCCTCTGTTGTTTACCCACATAACTATGGCTT
EST: gi|60354612|gb|DN221585.1|DN221585
EST:     GAGGCAGCAAGGTTAAGTACGAGTTGGACAAGGCATCTGGTCTGATCAAG                         GTGGACCGTGTTCTTTATTCCTCTGTTGTTTACCCACATAACTATGGCTTC
genomic: GAGGCAGCAAGGTTAAGTACGAGTTGGACAAGGCATCTGGTCTGATCAAGgtgagatcca ... cttgttacagGTGGACCGTGTTCTTTATTCCTCTGTTGTTTACCCACATAACTATGGCTTC

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: 46 (upstream exon), 49 (downstream exon)
Score: 52

AAACCTATCATGCACATTTTGTTTCAATTGTCAGGTGGTTGAGATTCCTAGAGGCAGCAAGGTTAAGTACGAGTTGGACAAGGCATCTGGTCTGATCAAGgtgagatcca ... cttgttacagGTGGACCGTGTTCTTTATTCCTCTGTTGTTTACCCACATAACTATGGCTTCATTCCACGCACACTCTGTGAGGATAACGACCCCCTGGATGTCCTCATAC


Block sizes: 46 (upstream exon), 48 (downstream exon)
Score: 40

AAACCTATCATGCACATTTTGTTTCAATTGTCAGGTGGTTGAGATTCCTAGAGGCAGCAAGGTTAAGTACGAGTTGGACAAGGCATCTGGTCTGATCAAGgtgagatcca ... cttgttacagGTGGACCGTGTTCTTTATTCCTCTGTTGTTTACCCACATAACTATGGCTTCATTCCACGCACACTCTGTGAGGATAACGACCCCCTGGATGTCCTCATAC


Block sizes: 47 (upstream exon), 49 (downstream exon)
Score: 18

AAACCTATCATGCACATTTTGTTTCAATTGTCAGGTGGTTGAGATTCCTAGAGGCAGCAAGGTTAAGTACGAGTTGGACAAGGCATCTGGTCTGATCAAGgtgagatcca ... cttgttacagGTGGACCGTGTTCTTTATTCCTCTGTTGTTTACCCACATAACTATGGCTTCATTCCACGCACACTCTGTGAGGATAACGACCCCCTGGATGTCCTCATAC


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 79

AAACCTATCATGCACATTTTGTTTCAATTGTCAGGTGGTTGAGATTCCTAGAGGCAGCAAGGTTAAGTACGAGTTGGACAAGGCATCTGGTCTGATCAAGgtgagatcca ... cttgttacagGTGGACCGTGTTCTTTATTCCTCTGTTGTTTACCCACATAACTATGGCTTCATTCCACGCACACTCTGTGAGGATAACGACCCCCTGGATGTCCTCATAC




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gctacatcttgtcttttcactttgacagtaggtaatcggatattacttgttacagGTGGACCGTGTTCTTTATTCCTCTGTTGTTTACCCACATAACTATGGCTTCATTCCACGCACACTCTGTGAGGATAACGACCCCCTGGATGTCCTCATAC
                   ctttgac  putative branch site (score: 79)
                                       atattactt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tgaatgttagtaacactaacacctagggttaaggtgggcttgcttgctacatcttgtcttttcactttgacagtaggtaatcggatattacttgttacagGTGGACCGTGTTCTTTATTCCTCTGTTGTTTACCCACATAACTATGGCTTCATTCCACGCACACTCTGTGAGGATAACGACCCCCTGGATGTCCTCATAC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGGAT