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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...aaacctagtttgataaaatttgggtatgctgtgctttgggtattcaaatgccttttggagcagtaaatcctgatcatctgtcatgtatccttttatttagGCACAGTTAATATACACCCAAGTTTGTTGCCTCTATATCGTGGTGCAGCTCCTGTGCAGAGGGCACTGCAG

Basic information

species Zea mays
transcript GRMZM2G019437_T01
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G019437_T01 (Zea mays), 3'ss of exon 3
lower sequence: LOC_Os01g49330.1 (Oryza sativa), 3'ss of exon 3
------aaacctagtttgataaaatttgggtatgctgtgctttgggtattcaaatgccttttggagcagtaaatcctgatcatctgtcatgtatccttttat-ttagGCACAGTTAATATACACCCAAGTTTGTTGCCTCTATATCGTGGTGCAGCTCCTGTGCAGAGGGCACTGCAG
       | |||| ||||  | || |    ||||       |||  | ||     | ||  || ||   | ||   |||  || || ||| | |   || ||   ||| || ||||| |||||||| |||||| |||||||||||||||||||||| ||||||||||||||| |||||
taaaagcagcctactttgccacaaatcaa-tatgggacatgttgaatttt-----gtctactg-agtgctgaacattgactatttggcatttctatcttcataccagGAACTGTTAACATACACCCGAGTTTGCTGCCTCTATATCGTGGTGCAGCACCTGTGCAGAGGGCATTGCAG

upper sequence: GRMZM2G019437_T01 (Zea mays), 3'ss of exon 3
lower sequence: AT1G66520.1 (Arabidopsis thaliana), 3'ss of exon 4
--------aaacctagtttgataaaatttgggtatgctgtgctttgggtattcaaatgccttttggagcagtaaatcctg-atcatctgtcatgtatccttttatttagGCACAGTTAATATACACCCAAGTTTGTTGCCTCTATATCGTGGTGCAGCTCCTGTGCAGAGGGCACTGCAG
        ||   | | |||||  | ||  || |     ||   |   | |  |   |     || |  | | | || ||  |  |    |   | |    |  |||||| ||||| || ||||||||||||||| |||| || || |||||||||||||| || || || ||| | |||
gttagttaaagaattggttgatggacttatggaaacgaatgtagtttctttatagtagatagctgca--aatgagtcttgtgttttgaagccaatgtttaatgttttagGGACAGTGAACATACACCCAAGTTTGCTGCCGCTGTACCGTGGTGCAGCTCCAGTTCAAAGAGCATTACAG

upper sequence: GRMZM2G019437_T01 (Zea mays), 3'ss of exon 3
lower sequence: Vv14s0006g01830.t01 (Vitis vinifera), 3'ss of exon 4
aaacctagtttgataaaatttgggtatgct-gtgctttgggta--ttcaaatgccttttggagcagtaaatcctgatcatctgtcatgt----atccttttatttagGCACAGTTAATATACACCCAAGTTTGTTGCCTCTATATCGTGGTGCAGCTCCTGTGCAGAGGGCACTGCAG
      |||     ||||    ||  ||||   |||  | ||   ||  |  |        |  |    || || |   | || |||||    ||    ||  | ||| ||||| ||||||||||||||| || ||||||| || |||||||| |||||||| || || ||| |||||
------agtaaataaaaaaacaggggtgctcaagctaagagttcttttcatcggggcccaaaaaatctgatactaaatttttg-catgtccaaatgtaatttctcagGAACAGTCAATATACACCCAAGTCTGCTGCCTCTGTACCGTGGTGCTGCTCCTGTTCAAAGAGCATTGCAG

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|31360881|gb|CD445238.1|CD445238
EST:     TGCTTACGGGAACATTCTGCCCCAGAAATTTCTTGATATCCCATCGTGCG                         GCACAGTTAATATACACCCAAGTTTGTTGCCTCTATATCGTGGTGCAGCTC
genomic: TGCTTACGGGAACATTCTGCCCCAGAAATTTCTTGATATCCCATCGTGCGgtacggctgg ... ttttatttagGCACAGTTAATATACACCCAAGTTTGTTGCCTCTATATCGTGGTGCAGCTC
EST: gi|67022687|gb|CO451436.1|CO451436
EST:     CGGGAAC-TTCTGCCCCANAAATTTCTTGATATCCCATCGTGCG                         GCACAGTTAATATACACCCAAGTTTGTTGCCTCTATATCGTGGTGCAGCTC
genomic: CGGGAACATTCTGCCCCAGAAATTTCTTGATATCCCATCGTGCGgtacggctgg ... ttttatttagGCACAGTTAATATACACCCAAGTTTGTTGCCTCTATATCGTGGTGCAGCTC
EST: gi|71420934|gb|DR805240.1|DR805240
EST:     TGCTTACGGGAACATTCTGCCCCAGAAATTTCTTGATATCCCATCGTGCG                         GCACAGTTAATATACACCCAAGTTTGTTGCCTCTATATCGTGGTGCAGCTC
genomic: TGCTTACGGGAACATTCTGCCCCAGAAATTTCTTGATATCCCATCGTGCGgtacggctgg ... ttttatttagGCACAGTTAATATACACCCAAGTTTGTTGCCTCTATATCGTGGTGCAGCTC
EST: gi|149076153|gb|EE164742.2|EE164742
EST:     TGCTTACGGGAACATTCTGCCCCAGAAATTTCTTGATATCCCATCGTGCG                         GCACAGTTAATATACACCCAAGTTTGTTGCCTCTATATCGTGGTGCAGCTC
genomic: TGCTTACGGGAACATTCTGCCCCAGAAATTTCTTGATATCCCATCGTGCGgtacggctgg ... ttttatttagGCACAGTTAATATACACCCAAGTTTGTTGCCTCTATATCGTGGTGCAGCTC
EST: gi|67023553|gb|CO452302.1|CO452302
EST:     CTTGATTTTCCATCGTGCG                         GCACAGTTAATATACACCCAAGTTTGTTGCCTCTATATCGTGGTGCAGCTC
genomic: CTTGATATCCCATCGTGCGgtacggctgg ... ttttatttagGCACAGTTAATATACACCCAAGTTTGTTGCCTCTATATCGTGGTGCAGCTC
EST: gi|94479122|gb|EB708080.1|EB708080
EST:     TGCTTACGGGAACATTCTGCCCCAGAAATTTCTTGATATCCCATCGTGCG                         GCACAGTTAATATACACCCAAGTTTGTTGCCTCTATATCGTGGTGCAGCTC
genomic: TGCTTACGGGAACATTCTGCCCCAGAAATTTCTTGATATCCCATCGTGCGgtacggctgg ... ttttatttagGCACAGTTAATATACACCCAAGTTTGTTGCCTCTATATCGTGGTGCAGCTC
EST: gi|211394070|gb|FL339831.1|FL339831
EST:     TGCTTACGGGAACATTCTGCCCCAGAAATTTCTTGATATCCCATCGTGCG                         GCACAGTTAATATACACCCAAGTTTGTTGCCTCTATATCGTGGTGCAGCTC
genomic: TGCTTACGGGAACATTCTGCCCCAGAAATTTCTTGATATCCCATCGTGCGgtacggctgg ... ttttatttagGCACAGTTAATATACACCCAAGTTTGTTGCCTCTATATCGTGGTGCAGCTC
EST: gi|50332369|gb|CO527495.1|CO527495
EST:     TGCTTACGGGAACATTCTGCCCCAGAAATTTCTTGATATCCCATCGTGCG                         GCACAGTTAATATACACCCAAGTTTGTTGCCTCTATATCGTGGTGCAGCTC
genomic: TGCTTACGGGAACATTCTGCCCCAGAAATTTCTTGATATCCCATCGTGCGgtacggctgg ... ttttatttagGCACAGTTAATATACACCCAAGTTTGTTGCCTCTATATCGTGGTGCAGCTC
EST: gi|76289469|gb|DV029037.1|DV029037
EST:     TGCTTACGGGAACATTCTGCCCCAGAAATTTCTTGATATCCCATCGTGCG                         GCACAGTTAATATACACCCAAGTTTGTTGCCTCTATATCGTGGTGCAGCTC
genomic: TGCTTACGGGAACATTCTGCCCCAGAAATTTCTTGATATCCCATCGTGCGgtacggctgg ... ttttatttagGCACAGTTAATATACACCCAAGTTTGTTGCCTCTATATCGTGGTGCAGCTC
EST: gi|148952757|gb|EC898739.2|EC898739
EST:     TGCTTACGGGAACATTCTGCCCCAGAAATTTCTTGATATCCCATCGTGCG                         GCACAGTTAATATACACCCAAGTTTGTTGCCTCTATATCGTGGTGCAGCTC
genomic: TGCTTACGGGAACATTCTGCCCCAGAAATTTCTTGATATCCCATCGTGCGgtacggctgg ... ttttatttagGCACAGTTAATATACACCCAAGTTTGTTGCCTCTATATCGTGGTGCAGCTC

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: 44 (upstream exon), 47 (downstream exon)
Score: 24

TCGTTCCTGTCGGCCTTGAAGGAAGTGGAACCGGATGTTTGCATAACTGCTGCTTACGGGAACATTCTGCCCCAGAAATTTCTTGATATCCCATCGTGCGgtacggctgg ... ttttatttagGCACAGTTAATATACACCCAAGTTTGTTGCCTCTATATCGTGGTGCAGCTCCTGTGCAGAGGGCACTGCAG


Block sizes: 43 (upstream exon), 46 (downstream exon)
Score: 23

TCGTTCCTGTCGGCCTTGAAGGAAGTGGAACCGGATGTTTGCATAACTGCTGCTTACGGGAACATTCTGCCCCAGAAATTTCTTGATATCCCATCGTGCGgtacggctgg ... ttttatttagGCACAGTTAATATACACCCAAGTTTGTTGCCTCTATATCGTGGTGCAGCTCCTGTGCAGAGGGCACTGCAG


Block sizes: 43 (upstream exon), 45 (downstream exon)
Score: 8

TCGTTCCTGTCGGCCTTGAAGGAAGTGGAACCGGATGTTTGCATAACTGCTGCTTACGGGAACATTCTGCCCCAGAAATTTCTTGATATCCCATCGTGCGgtacggctgg ... ttttatttagGCACAGTTAATATACACCCAAGTTTGTTGCCTCTATATCGTGGTGCAGCTCCTGTGCAGAGGGCACTGCAG


Block sizes: 43 (upstream exon), 44 (downstream exon)
Score: 13

TCGTTCCTGTCGGCCTTGAAGGAAGTGGAACCGGATGTTTGCATAACTGCTGCTTACGGGAACATTCTGCCCCAGAAATTTCTTGATATCCCATCGTGCGgtacggctgg ... ttttatttagGCACAGTTAATATACACCCAAGTTTGTTGCCTCTATATCGTGGTGCAGCTCCTGTGCAGAGGGCACTGCAG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aaatgccttttggagcagtaaatcctgatcatctgtcatgtatccttttatttagGCACAGTTAATATACACCCAAGTTTGTTGCCTCTATATCGTGGTGCAGCTCCTGTGCAGAGGGCACTGCAG
                      tcctgat  putative branch site (score: 13)
                                          tccttttattt  putative PPT
                                        tatccttttattta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
aaacctagtttgataaaatttgggtatgctgtgctttgggtattcaaatgccttttggagcagtaaatcctgatcatctgtcatgtatccttttatttagGCACAGTTAATATACACCCAAGTTTGTTGCCTCTATATCGTGGTGCAGCTCCTGTGCAGAGGGCACTGCAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CAGCTC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CTGCAG
- - - - - - - - - - - - tatgctg
- - - - - - - - - - - - - - - -tgctttg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - ggagcag
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -catgtat