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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tttacagcccttgaaatatactaatgtttttgccttggtgtacaaaattattttatctcatgttttcagttattttatcctaaaatgactttcgttgcagGGTGTTCCAAATCCAAAGGCTATTCATTCTTCCAAAGCCGTGGGAGAGCCACCATTTTTCCTAGGTTCCGCCGTCTTATTTGCGATAAAGGATGCGATCT

Basic information

species Zea mays
transcript GRMZM2G050984_T01
intron # 9
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G050984_T01 (Zea mays), 3'ss of exon 9
lower sequence: LOC_Os03g31550.2 (Oryza sativa), 3'ss of exon 13
-tttacagcccttgaaatat-actaatgtttttgccttggtgta-caaaattattttatctcatgttttcagttatt-ttatcctaaaatgactttcgttgcagGGTGTTCCAAATCCAAAGGCTATTCATTCTTCCAAAGCCGTGGGAGAGCCACCATTTTTCCTAGGTTCCGCCGTCTTATTTGCGATAAAGGATGCGATCT
   |  |    || |  ||  |  || | |  ||  ||| |  |   | |||  | ||||  |  | |  | | |   || |  |    |   ||||||| ||||| |||   ||||||||||  ||||| || ||||| || || ||||||||||| |||||||| ||||| |||||||| ||||| |||||||||||||| |
tcatctaaaaattaatttaccagaaacgctcctgaattgtttcaatgacatttatctatcctacatctcgattcacagttgtttt----ttcttttcgttacagGGCGTTTTGAATCCAAAGGTCATTCACTCATCCAAGGCTGTAGGAGAGCCACCGTTTTTCCTCGGTTCAGCCGTCTTGTTTGCCATAAAGGATGCGATAT

upper sequence: GRMZM2G050984_T01 (Zea mays), 3'ss of exon 9
lower sequence: Vv06s0004g02030.t01 (Vitis vinifera), 3'ss of exon 13
tttacagcccttgaaatatactaatgtttttgccttggtgta-caaaattattttatctcatgttttcagttattttatcctaaaatgactttcgttgcagGGTGTTCCAAATCCAAAGGCTATTCATTCTTCCAAAGCCGTGGGAGAGCCACCATTTTTCCTAGGTTCCGCCGTCTTATTTGCGATAAAGGATGCGATCT
  |  | |   | ||| | | |  ||   | |      |  | | ||| |||||||  |  || ||||  ||  |  || |     |   ||   |  ||||||| ||||||||||||||| || ||||| ||||| || ||||| ||||| |||||||| || | |||| | ||||| || || || || ||||| ||  
gatcaatcatattaaacagaatgttgcagtagttcatttaaatctaaaatattttacattgtgatttctcttgctc-atgcgtttttatgttatctgacagGGTGCTCCAAATCCAAAGGCCATCCATTCATCCAAGGCTGTGGGTGAGCCTCCATTTTTTCTGGCTTCCTCTGTCTTCTTCGCCATCAAAGATGCAATTG
















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|78023990|gb|DV492377.1|DV492377
EST:     TACCCTCTGTAAATGATATACCTCTGAATTTCAAGGTTTCTCTATTAAAG                         GGTGTTCCAAATCCAAAGGCTATTCATTCTTCCAAAGCCGTGGGAGAGCCA
genomic: TACCCTCTGTAAATGATATACCTCTGAATTTCAAGGTTTCTCTATTAAAGgtaaatatat ... ttcgttgcagGGTGTTCCAAATCCAAAGGCTATTCATTCTTCCAAAGCCGTGGGAGAGCCA
EST: gi|60395383|gb|DN228252.1|DN228252
EST:     TACCCTCTGTAAATGATATACCTCTGAATTTCAAGGTTTCTCTATTAAAG                         GGTGTTCCAAATCCAAAGGCTATTCATTCTTCCAAAGCCGTGGGAGAGCCA
genomic: TACCCTCTGTAAATGATATACCTCTGAATTTCAAGGTTTCTCTATTAAAGgtaaatatat ... ttcgttgcagGGTGTTCCAAATCCAAAGGCTATTCATTCTTCCAAAGCCGTGGGAGAGCCA
EST: gi|67016938|gb|CO445687.1|CO445687
EST:     TACCCTCTGTAAATGATATACCTCTGAATTTCAAGGTTTCTCTATTAAAG                         GGTGTTCCAAATCCAAAGGCTATTCATTCTTCCAAAGCCGTGGGAGAGCCA
genomic: TACCCTCTGTAAATGATATACCTCTGAATTTCAAGGTTTCTCTATTAAAGgtaaatatat ... ttcgttgcagGGTGTTCCAAATCCAAAGGCTATTCATTCTTCCAAAGCCGTGGGAGAGCCA
EST: gi|14204330|gb|BG838007.1|BG838007
EST:     TACCCTCTGTAAATGATATACCTCTGAATTTCAAGGTTTCTCTATTAAAG                         GGTGTTCCAAATCCAAAGGCTATTCATTCTTCCAAAGCCGTGGGAGAGCCA
genomic: TACCCTCTGTAAATGATATACCTCTGAATTTCAAGGTTTCTCTATTAAAGgtaaatatat ... ttcgttgcagGGTGTTCCAAATCCAAAGGCTATTCATTCTTCCAAAGCCGTGGGAGAGCCA
EST: gi|14204197|gb|BG837874.1|BG837874
EST:     TACCCTCTGTAAATGATATACCTCTGAATTTCAAGGTTTCTCTATTAAAG                         GGTGTTCCAAATCCAAAGGCTATTCATTCTTCCAAAGCCGTGGGAGAGCCA
genomic: TACCCTCTGTAAATGATATACCTCTGAATTTCAAGGTTTCTCTATTAAAGgtaaatatat ... ttcgttgcagGGTGTTCCAAATCCAAAGGCTATTCATTCTTCCAAAGCCGTGGGAGAGCCA
EST: gi|45567638|gb|CK985669.1|CK985669
EST:     TACCCTCTGTAAATGATATACCTCTGAATTTCAAGGTTTCTCTATTAAAG                         GGTGTTCCAAATCCAAAGGCTATTCATTCTTCCAAAGCCGTGGGAGAGCCA
genomic: TACCCTCTGTAAATGATATACCTCTGAATTTCAAGGTTTCTCTATTAAAGgtaaatatat ... ttcgttgcagGGTGTTCCAAATCCAAAGGCTATTCATTCTTCCAAAGCCGTGGGAGAGCCA
EST: gi|211338067|gb|FL010980.1|FL010980
EST:     TACCCTCTGTAAATGATATACCTCTCAATTTCAAGGTTTCTCTATTAAAG                         GGTGTTCCAAATCCAAAGGCTATTCATTCTTCCAAAGCCGTGGGAGAGCCA
genomic: TACCCTCTGTAAATGATATACCTCTGAATTTCAAGGTTTCTCTATTAAAGgtaaatatat ... ttcgttgcagGGTGTTCCAAATCCAAAGGCTATTCATTCTTCCAAAGCCGTGGGAGAGCCA
EST: gi|78023637|gb|DV492024.1|DV492024
EST:     TACCCTCTGTAAATGATATACCTTTGAATTTCAAGGTTTCTCTATTAAAG                         GGTGTTCCAAATCCAAAGGCTATTCATTCTTCCAAAGCCGTGGGAGAGCCA
genomic: TACCCTCTGTAAATGATATACCTCTGAATTTCAAGGTTTCTCTATTAAAGgtaaatatat ... ttcgttgcagGGTGTTCCAAATCCAAAGGCTATTCATTCTTCCAAAGCCGTGGGAGAGCCA
EST: gi|6022258|gb|AW067186.1|AW067186
EST:     TACCCTCTGTAAATGATATACCTCTGAATTTCAAGGTTTCTCTATTAAAG                         GGTGTTCCAAATCCAAAGGCTATTCATTCTTCCAAAGCCGTGGGAGAGCCA
genomic: TACCCTCTGTAAATGATATACCTCTGAATTTCAAGGTTTCTCTATTAAAGgtaaatatat ... ttcgttgcagGGTGTTCCAAATCCAAAGGCTATTCATTCTTCCAAAGCCGTGGGAGAGCCA

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), 44 (downstream exon)
Score: 63

GTGGATTCGACCTGGACACCTCTTCACCTGCGGTCCTGGTTCTTACAAAATACCCTCTGTAAATGATATACCTCTGAATTTCAAGGTTTCTCTATTAAAGgtaaatatat ... ttcgttgcagGGTGTTCCAAATCCAAAGGCTATTCATTCTTCCAAAGCCGTGGGAGAGCCACCATTTTTCCTAGGTTCCGCCGTCTTATTTGCGATAAAGGATGCGATCT


Block sizes: 49 (upstream exon), 46 (downstream exon)
Score: 163

GTGGATTCGACCTGGACACCTCTTCACCTGCGGTCCTGGTTCTTACAAAATACCCTCTGTAAATGATATACCTCTGAATTTCAAGGTTTCTCTATTAAAGgtaaatatat ... ttcgttgcagGGTGTTCCAAATCCAAAGGCTATTCATTCTTCCAAAGCCGTGGGAGAGCCACCATTTTTCCTAGGTTCCGCCGTCTTATTTGCGATAAAGGATGCGATCT


Block sizes: 49 (upstream exon), 43 (downstream exon)
Score: 100

GTGGATTCGACCTGGACACCTCTTCACCTGCGGTCCTGGTTCTTACAAAATACCCTCTGTAAATGATATACCTCTGAATTTCAAGGTTTCTCTATTAAAGgtaaatatat ... ttcgttgcagGGTGTTCCAAATCCAAAGGCTATTCATTCTTCCAAAGCCGTGGGAGAGCCACCATTTTTCCTAGGTTCCGCCGTCTTATTTGCGATAAAGGATGCGATCT


Block sizes: 48 (upstream exon), 43 (downstream exon)
Score: 62

GTGGATTCGACCTGGACACCTCTTCACCTGCGGTCCTGGTTCTTACAAAATACCCTCTGTAAATGATATACCTCTGAATTTCAAGGTTTCTCTATTAAAGgtaaatatat ... ttcgttgcagGGTGTTCCAAATCCAAAGGCTATTCATTCTTCCAAAGCCGTGGGAGAGCCACCATTTTTCCTAGGTTCCGCCGTCTTATTTGCGATAAAGGATGCGATCT




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aattattttatctcatgttttcagttattttatcctaaaatgactttcgttgcagGGTGTTCCAAATCCAAAGGCTATTCATTCTTCCAAAGCCGTGGGAGAGCCACCATTTTTCCTAGGTTCCGCCGTCTTATTTGCGATAAAGGATGCGATCT
                                tcctaaa  putative branch site (score: 62)
                                           ctttcgtt  putative PPT
                        ttattttatcctaaaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tttacagcccttgaaatatactaatgtttttgccttggtgtacaaaattattttatctcatgttttcagttattttatcctaaaatgactttcgttgcagGGTGTTCCAAATCCAAAGGCTATTCATTCTTCCAAAGCCGTGGGAGAGCCACCATTTTTCCTAGGTTCCGCCGTCTTATTTGCGATAAAGGATGCGATCT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGGATG
- - - - - - - - - - - - - - - tgccttg
- - - - - - - - - - - - - - - - - - - - tacaaaa