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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gctgtgttttaaactttaaaaatttcattgttagattcataatggtttaactattgagattcaacatatttctgaagtttcaattgatatttcttctcagATGACAAGGAGAAACCAACACATTTGAGATTTCTAGTGTCTAATACGGCAGCAGGGTGCATCATTGGCAAGGGTGGATCAACCATTAATGATTTTCAGTC

Basic information

species Zea mays
transcript GRMZM2G008410_T01
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G008410_T01 (Zea mays), 3'ss of exon 1
lower sequence: LOC_Os02g57640.1 (Oryza sativa), 3'ss of exon 1
-gctgtgttttaaactttaaaaatttcattgttagattcataatggtttaactattgagattcaacatatttctgaagtttcaattgatatttcttctcagATGACAAGGAGAAACCAACACATTTGAGATTTCTAGTGTCTAATACGGCAGCAGGGTGCATCATTGGCAAGGGTGGATCAACCATTAATGATTTTCAGTC
        |||      |||| |  | || |   |     |  | |     ||  |    | | |  || ||||||| || ||| ||||  |||| | |||||||||||||||| ||||| ||| |||| ||||| || || || ||||||||||| ||||| ||||||||||||||||||||||||||||| ||||||||
aaaaacaattttgtgcctaaacaaataatggcatgcacagtttttggccctctcctttattgcta-gtaattctgaatttccaagtgatcattctccacagATGACAAGGAGAAGCCAACCCATCTGAGGTTTCTGGTATCAAACACGGCAGCAGGATGCATTATTGGCAAGGGTGGATCAACCATTAATGAATTTCAGTC

upper sequence: GRMZM2G008410_T01 (Zea mays), 3'ss of exon 1
lower sequence: Vv13s0019g05360.t01 (Vitis vinifera), 3'ss of exon 3
--gctgtgttttaaactttaaaaatttcattgttagattcataatggtttaactattgagattcaacatatttctgaagtttcaattgatatttcttctcagATGACAAGGAGAAACCAACACATTTGAGATTTCTAGTGTCTAATACGGCAGCAGGGTGCATCATTGGCAAGGGTGGATCAACCATTAATGATTTTCAGTC
  |   |||| | ||    |   |||    ||  | ||  |   | | |||  |      | | | || |||| |    |||    || | | |  | ||||||   | ||||||  | ||| |  | |||||||| || || ||| | ||||| || |   | ||||| |||||||| ||||| |||||||||||||||||
aaggcatgttatcaatggcatgcattaagatga-acatgtaggcttgcttacttcccttcactaatca-atttgtcttcttttttatgctttctactgtcagATTTTATGGAGAAGTCTACATACATTAGATTTCTTGTATCAAATGCTGCAGCTGGTTCTGTAATTGGAAAGGGTGGTTCAACTATTAATGATTTTCAGTC
















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|87152714|gb|DY397503.1|DY397503
EST:     TGCCCCACGCTCCCCTCCGCAGCAGCAGCAGTCTCCCTCCGAGGAAGGAG                         ATGACAAGGAGAAACCAACACATTTGAGATTTCTAGTGTCTAATACGGCAG
genomic: TGCCCCACGCTCCCCTCCGCAGCAGCAGCAGTCTCCCTCCGAGGAAGGAGgtaactgcca ... ttcttctcagATGACAAGGAGAAACCAACACATTTGAGATTTCTAGTGTCTAATACGGCAG
EST: gi|22491469|gb|BU051392.1|BU051392
EST:     TGCCCCACGCTCCCCTCCGCAGCAGCAGCAGTCTCCCTCCGAGGAAGGAG                         ATGACAAGGAGAAACCAACACATTTGAGATTTCTAGTGTCTAATACGGCAG
genomic: TGCCCCACGCTCCCCTCCGCAGCAGCAGCAGTCTCCCTCCGAGGAAGGAGgtaactgcca ... ttcttctcagATGACAAGGAGAAACCAACACATTTGAGATTTCTAGTGTCTAATACGGCAG
EST: gi|19350719|gb|BM895251.1|BM895251
EST:     TGCCCCACGCTCCCCTCCGCAGCAGCAGCAGTCTCCCTCCGAGGAAGGAG                         ATGACAAGGAGAAACCAACACATTTGAGATTTCTAGTGTCTAATACGGCAG
genomic: TGCCCCACGCTCCCCTCCGCAGCAGCAGCAGTCTCCCTCCGAGGAAGGAGgtaactgcca ... ttcttctcagATGACAAGGAGAAACCAACACATTTGAGATTTCTAGTGTCTAATACGGCAG
EST: gi|9028619|gb|BE238659.1|BE238659
EST:     TGCCCCACGCTCCCCTCCGCAGCAGCAGCAGTCTCCCTCCGAGGAAGGAG                         ATGACAAGGAGAAACCAACACATTTGAGATTTCTAGTGTCTAATACTGTAG
genomic: TGCCCCACGCTCCCCTCCGCAGCAGCAGCAGTCTCCCTCCGAGGAAGGAGgtaactgcca ... ttcttctcagATGACAAGGAGAAACCAACACATTTGAGATTTCTAGTGTCTAATACGGCAG
EST: gi|148995842|gb|EE035078.2|EE035078
EST:     TGCCCCACGCTCCCCTCCGCAGCAGCAGCAGTCTCCCTCCGAGGAAGGAG                         ATGACAAGGAGAAACCAACACATTTGAGATTTCTAGTGTCTAATACGGCAG
genomic: TGCCCCACGCTCCCCTCCGCAGCAGCAGCAGTCTCCCTCCGAGGAAGGAGgtaactgcca ... ttcttctcagATGACAAGGAGAAACCAACACATTTGAGATTTCTAGTGTCTAATACGGCAG
EST: gi|19350720|gb|BM895252.1|BM895252
EST:     TGCCCCACGCTCCCCTCCGCAGCAGCAGCAGTCTCCCTCCGAGGAAGGAG                         ATGACAAGGAGAAACCAACACATTTGAGATTTCTAGTGTCTAATACGGCAG
genomic: TGCCCCACGCTCCCCTCCGCAGCAGCAGCAGTCTCCCTCCGAGGAAGGAGgtaactgcca ... ttcttctcagATGACAAGGAGAAACCAACACATTTGAGATTTCTAGTGTCTAATACGGCAG
EST: gi|78114793|gb|DV533181.1|DV533181
EST:     TGCCCCACGCTCCCCTCCGCAGCAGCAGCAGTCTCCCTCCGAGGAAGGAG                         ATGACAAGGAGAAACCAACACATTTGAGATTTCTAGTGTCTAATACGGCAG
genomic: TGCCCCACGCTCCCCTCCGCAGCAGCAGCAGTCTCCCTCCGAGGAAGGAGgtaactgcca ... ttcttctcagATGACAAGGAGAAACCAACACATTTGAGATTTCTAGTGTCTAATACGGCAG

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: 325

GAAGCCCCGGGCTCCCCCTACGCCTCCTCGCCGGAATCCGCCCCCAAGCGTGCCCCACGCTCCCCTCCGCAGCAGCAGCAGTCTCCCTCCGAGGAAGGAGgtaactgcca ... ttcttctcagATGACAAGGAGAAACCAACACATTTGAGATTTCTAGTGTCTAATACGGCAGCAGGGTGCATCATTGGCAAGGGTGGATCAACCATTAATGATTTTCAGTC


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 201

GAAGCCCCGGGCTCCCCCTACGCCTCCTCGCCGGAATCCGCCCCCAAGCGTGCCCCACGCTCCCCTCCGCAGCAGCAGCAGTCTCCCTCCGAGGAAGGAGgtaactgcca ... ttcttctcagATGACAAGGAGAAACCAACACATTTGAGATTTCTAGTGTCTAATACGGCAGCAGGGTGCATCATTGGCAAGGGTGGATCAACCATTAATGATTTTCAGTC


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 250

GAAGCCCCGGGCTCCCCCTACGCCTCCTCGCCGGAATCCGCCCCCAAGCGTGCCCCACGCTCCCCTCCGCAGCAGCAGCAGTCTCCCTCCGAGGAAGGAGgtaactgcca ... ttcttctcagATGACAAGGAGAAACCAACACATTTGAGATTTCTAGTGTCTAATACGGCAGCAGGGTGCATCATTGGCAAGGGTGGATCAACCATTAATGATTTTCAGTC


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 210

GAAGCCCCGGGCTCCCCCTACGCCTCCTCGCCGGAATCCGCCCCCAAGCGTGCCCCACGCTCCCCTCCGCAGCAGCAGCAGTCTCCCTCCGAGGAAGGAGgtaactgcca ... ttcttctcagATGACAAGGAGAAACCAACACATTTGAGATTTCTAGTGTCTAATACGGCAGCAGGGTGCATCATTGGCAAGGGTGGATCAACCATTAATGATTTTCAGTC




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tttaactattgagattcaacatatttctgaagtttcaattgatatttcttctcagATGACAAGGAGAAACCAACACATTTGAGATTTCTAGTGTCTAATACGGCAGCAGGGTGCATCATTGGCAAGGGTGGATCAACCATTAATGATTTTCAGTC
                                          tatttcttctc  CT-rich tract
                                tttcaattgatattt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gctgtgttttaaactttaaaaatttcattgttagattcataatggtttaactattgagattcaacatatttctgaagtttcaattgatatttcttctcagATGACAAGGAGAAACCAACACATTTGAGATTTCTAGTGTCTAATACGGCAGCAGGGTGCATCATTGGCAAGGGTGGATCAACCATTAATGATTTTCAGTC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGTGGA
- tgtgttt
- - - - - - - - - - - tttcatt