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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...caccgaagccttttgcgtttgtgatatgatatgttttattgagttgcttctggacccatagtcccatgctaacaatttatgagggaaaaaatgctgacagGAAGAAGAAGGCAGTCCACAAGACCGCAACCACCGATGACAAGCGGCTTCAGAGCACGTTGAAAAGAATTGGAGTGAACACTATTCCTGGTATTGAGGAG

Basic information

species Zea mays
transcript GRMZM2G041881_T02
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G041881_T01 (Zea mays), 3'ss of exon 2
lower sequence: LOC_Os03g01910.1 (Oryza sativa), 3'ss of exon 2
----caccgaagccttttgcgtttgtgatatgatatgtt--ttattgagttgcttctggacccatagtcccatgctaacaatttatgagggaaaaaatgctgacagGAAGAAGAAGGCAGTCCACAAGACCGCAACCACCGATGACAAGCGGCTTCAGAGCACGTTGAAAAGAATTGGAGTGAACACTATTCCTGGTATTGAGGAG
     |     | ||| |   |||| |||  ||| | ||    | ||  |||      | ||  | |   |||  ||| | ||  || |      | |  || |||||||||||||||||| ||||||||  | ||||| ||||||||| ||||||| ||||| ||||||||| | ||||||||||  ||||||||||| || |||
aagatatactgggcttgtat-tttgggatccgatcttttaaacaatgtattgtgctgtggcctttggattcatattaatacttgttgtgc-----atttatggcagGAAGAAGAAGGCAGTTCACAAGACTACCACCACTGATGACAAGAGGCTTCAAAGCACCTTGAAAAGAGTAGGAGTGAACAACATTCCTGGTATCGAAGAG

upper sequence: GRMZM2G041881_T01 (Zea mays), 3'ss of exon 2
lower sequence: GLYMA11G12170.1 (Glycine max), 3'ss of exon 2
caccgaagccttttgcgtttgtgatatgatatgttttattgagttgcttctggacccatagtcccatgctaacaatttatgagggaaaaaatgctga---cagGAAGAAGAAGGCAGTCCACAAGACCGCAACCACCGATGACAAGCGGCTTCAGAGCACGTTGAAAAGAATTGGAGTGAACACTATTCCTGGTATTGAGGAG
    | || |  || |||| |   |||  | | | | ||| |        || | |  | ||          |  || |||         ||| |      || ||||||||||| |||||||||||  ||||||| ||||||||  |||||||||||||  |||| ||||| || |||||  | || || | ||||||||||
gtttgcagtcaatt-cgttggctttat--tttttgtaattaaacacaaaatgaatctgttgtgttgaaagttctcttaatgttttgtcttatgttcggtctagAAAGAAGAAGGCTGTCCACAAGACAACAACCACAGATGACAAAAGGCTTCAGAGCACCCTGAAGAGAATAGGGGTGAATGCCATCCCGGCTATTGAGGAG

upper sequence: GRMZM2G041881_T01 (Zea mays), 3'ss of exon 2
lower sequence: GLYMA12G04380.1 (Glycine max), 3'ss of exon 2
-caccgaagccttttgcgtttgtgatatgatatgttttattgagttgcttctggacccatagtcccatgctaacaatttatgagggaaaaaatgctgac---agGAAGAAGAAGGCAGTCCACAAGACCGCAACCACCGATGACAAGCGGCTTCAGAGCACGTTGAAAAGAATTGGAGTGAACACTATTCCTGGTATTGAGGAG
 |||  ||    || || |||  | | |    | |   |||||        || | |  | ||          |  ||||||         ||| |      || ||||||||||| |||||||||||  ||||||| ||||||||  |||||||||||||  |||| ||||| || |||||  | || |||| |||||| |||
tcactcaatttgttggctttttagtttt----tttggaattgaacacaaaatgcatctgttgtgttgaatgctctctttatgttttgtcttatgtttgttctagAAAGAAGAAGGCTGTCCACAAGACAACAACCACAGATGACAAAAGGCTTCAGAGCACCCTGAAGAGAATAGGGGTGAATGCCATCCCTGCTATTGAAGAG

upper sequence: GRMZM2G041881_T01 (Zea mays), 3'ss of exon 2
lower sequence: GLYMA11G12180.1 (Glycine max), 3'ss of exon 2
caccgaagccttttgcgtttgtgatatgatatgttttattgagttgcttctggacccatagtcccatgctaacaatttatgagggaaaaaatgctga---cagGAAGAAGAAGGCAGTCCACAAGACCGCAACCACCGATGACAAGCGGCTTCAGAGCACGTTGAAAAGAATTGGAGTGAACACTATTCCTGGTATTGAGGAG
    | || |  || |||| |   || | | | | | ||| |        || |    | ||          |  || |||         |||||      || ||||||||||| |||||||||||  ||||||| ||||||||  |||||||||||||  |||| ||||| || |||||  | || || | ||||||||||
-tttgcagtcaatt-cgttggcttta-gttttttataattaaacacaaaatgtatttgttgtgttgaaagttctcttaatgttttgtcttatgctcggtctagAAAGAAGAAGGCTGTCCACAAGACAACAACCACAGATGACAAAAGGCTTCAGAGCACCCTGAAGAGAATAGGGGTGAATGCCATCCCGGCTATTGAGGAG

upper sequence: GRMZM2G041881_T01 (Zea mays), 3'ss of exon 2
lower sequence: AT1G73230.1 (Arabidopsis thaliana), 3'ss of exon 2
caccgaagccttttgcgtttgtgatatgatatgttttattgagttgcttctggacccatagtcccatgctaacaatttatgagggaaaaaatgctgacagGAAGAAGAAGGCAGTCCACAAGACCGCAACCACCGATGACAAGCGGCTTCAGAGCACGTTGAAAAGAATTGGAGTGAACACTATTCCTGGTATTGAGGAG
      |  | |||  || | |  | ||| || | |  ||  |    || |      ||| || |     |||| |||         |   |  |  ||| ||||||||||| || ||||||||| | || |||||||||||| |||| ||||||||  | || ||| ||||||| ||  | ||||| |  ||||| || 
--gtatactcatttatgtcttttctgtga-atttgtgtttttgccatttttcatgttatattctc---taaacattttg--------actctcatttcagAAAGAAGAAGGCTGTTCACAAGACCACTACAACCGATGACAAGAGGCTCCAGAGCACTCTTAAGAGAGTTGGAGTCAATTCCATTCCCGCCATTGAAGAA

upper sequence: GRMZM2G041881_T01 (Zea mays), 3'ss of exon 2
lower sequence: PP1S28_196V6.1 (Physcomitrella patens), 3'ss of exon 2
caccgaagccttttgcgtttgtgatatgatatgttttattgagt-tgcttctggacccata-gtcccatgctaacaatttatgagggaaaaaat--gctga-cagGAAGAAGAAGGCAGTCCACAAGACCGCAACCACCGATGACAAGCGGCTTCAGAGCACGTTGAAAAGAATTGGAGTGAACACTATTCCTGGTATTGAGGAG
       | ||  | | |||||  |    | ||      || |  |    || | | |||  | || |||    | |    ||        |||  ||||| |||||||||||| || || ||||||||| | ||||| || |||||| || | |||||||| |||||  || | ||||||||||| ||||| || ||||| |||
----ttcgtctgctac-tttgtactgctttgtgaggctctgggagtttccctagtctcatgtgccctatgtggtctacccttgtcaatttcaattggctgaacagGAAGAAGAAAGCTGTTCACAAGACCACCACCACTGACGACAAGAGGTTGCAGAGCACCTTGAAGCGACTCGGAGTGAACACCATTCCCGGAATTGAAGAG

upper sequence: GRMZM2G041881_T01 (Zea mays), 3'ss of exon 2
lower sequence: EFJ21066 (Selaginella moellendorffii), 3'ss of exon 1
caccgaagccttttgcgtttgtgatatgatatgttttattgagttgcttctggacccatagtcccatgctaacaattta-tgagggaaaaaatgctgacagGAAGAAGAAGGCAGTCCACAAGACCGCAACCACCGATGACAAGCGGCTTCAGAGCACGTTGAAAAGAATTGGAGTGAACACTATTCCTGGTATTGAGGAG
                                                |   ||       |   ||   || | |||  ||||           |  |||||||||||||||||| ||||||||||| |||||||| |||||| || | || | |||| | || ||| | || || ||||| || || || |||||||||
-----------------------------------------------gtaaagatttgggattagattggaagattttggtgagaattctggcaatcgcagGAAGAAGAAGGCAGTGCACAAGACCGCGACCACCGACGACAAGAGGTTGCAAAACACGCTCAAGAGATTGGGCGTCAACACCATCCCCGGCATTGAGGAG

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|211164811|gb|FL068780.1|FL068780
EST:     AAGAAGATGGCGGGTGCTGTGCGCACTGGAGGAAAGGGCAGCATGCGCAG                         GAAGAAGAAGGCAGCCCACAAGACCGCAACCACCGA
genomic: AAGAAGATGGCGGGTGCTGTGCGCACTGGAGGAAAGGGCAGCATGCGCAGgtgcctcatc ... atgctgacagGAAGAAGAAGGCAGTCCACAAGACCGCAACCACCGA
EST: gi|211164808|gb|FL068777.1|FL068777
EST:     AAGAAGATGGCGGGTGCTGTGCGCACTGGAGGAAAGGGCAGCATGCGCAG                         GAAGAAGAAGGCAGTCCACAAGACCGCAACCACCGATGACAAGCGGCTTCA
genomic: AAGAAGATGGCGGGTGCTGTGCGCACTGGAGGAAAGGGCAGCATGCGCAGgtgcctcatc ... atgctgacagGAAGAAGAAGGCAGTCCACAAGACCGCAACCACCGATGACAAGCGGCTTCA
EST: gi|15426682|gb|BI542504.1|BI542504
EST:     GAAGATGGCGGGTGCTGTGCGCACTGGAGGAAAGGGCAGCATGCGCAG                         GAAGAAGAAGGCAGTCCACAAGACCGCAACCACCGATGACAAGCGGCTTCA
genomic: GAAGATGGCGGGTGCTGTGCGCACTGGAGGAAAGGGCAGCATGCGCAGgtgcctcatc ... atgctgacagGAAGAAGAAGGCAGTCCACAAGACCGCAACCACCGATGACAAGCGGCTTCA
EST: gi|211164799|gb|FL068768.1|FL068768
EST:     AAGAAGATGGCGGGTGCTGTGCGCACTGGAGGAAAGGGCAGCATGCGCAG                         GAAGAAGAAGGCAGTCCACAAGACCGCAACCACCGATGACAAGCGGCTTCA
genomic: AAGAAGATGGCGGGTGCTGTGCGCACTGGAGGAAAGGGCAGCATGCGCAGgtgcctcatc ... atgctgacagGAAGAAGAAGGCAGTCCACAAGACCGCAACCACCGATGACAAGCGGCTTCA
EST: gi|211339244|gb|FL068784.1|FL068784
EST:     AAGAAGATGGCGGGTGCTGTGCGCACTGGAGGAAAGGGCAGCATGCGCAG                         GAAGAAGAAGGCAGTCCACAAGACCGCAACCACCGATGACAAGCGGCTTCA
genomic: AAGAAGATGGCGGGTGCTGTGCGCACTGGAGGAAAGGGCAGCATGCGCAGgtgcctcatc ... atgctgacagGAAGAAGAAGGCAGTCCACAAGACCGCAACCACCGATGACAAGCGGCTTCA
EST: gi|13490637|gb|BG517401.1|BG517401
EST:     AGATGGCGGGTGCTGTGCGCACTGGAGGAAAGGGCAGCATGCGCAG                         GAAGAAGAAGGCAGTCCACAAGACCGCAACCACCGATGACAAGCGGCTTCA
genomic: AGATGGCGGGTGCTGTGCGCACTGGAGGAAAGGGCAGCATGCGCAGgtgcctcatc ... atgctgacagGAAGAAGAAGGCAGTCCACAAGACCGCAACCACCGATGACAAGCGGCTTCA
EST: gi|14997050|gb|BI319140.1|BI319140
EST:     AAGAAGATGGCGGGTGCTGTGCGCACTGGAGGAAAGGGCAGCATGCGCAG                         GAAGAAGAAGGCAGTCCACAAGACCGCAACCACCGATGACAAGCGGCTTCA
genomic: AAGAAGATGGCGGGTGCTGTGCGCACTGGAGGAAAGGGCAGCATGCGCAGgtgcctcatc ... atgctgacagGAAGAAGAAGGCAGTCCACAAGACCGCAACCACCGATGACAAGCGGCTTCA
EST: gi|211530342|gb|FL172605.1|FL172605
EST:     AAGAAGATGGCGGGTGCTGTGCGCACTGGAGGAAAGGGCAGCATGCGCAG                         GAAGAAGAAGGCAGTCCACAAGACCGCAACCACCG
genomic: AAGAAGATGGCGGGTGCTGTGCGCACTGGAGGAAAGGGCAGCATGCGCAGgtgcctcatc ... atgctgacagGAAGAAGAAGGCAGTCCACAAGACCGCAACCACCG
EST: gi|76016587|gb|DT943757.1|DT943757
EST:     AAGAAGATGGCGGGTGCTGTGCGCACTGGAGGAAAGGGCAGCATGCGCAG                         GAAGAAGAAGGCAGTCCACAAGACCGCAACCACCGATGACAAGCGGCTTCA
genomic: AAGAAGATGGCGGGTGCTGTGCGCACTGGAGGAAAGGGCAGCATGCGCAGgtgcctcatc ... atgctgacagGAAGAAGAAGGCAGTCCACAAGACCGCAACCACCGATGACAAGCGGCTTCA

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: 452

ATGAATGTGGAGAAGCTCAAGAAGATGGCGGGTGCTGTGCGCACTGGAGGAAAGGGCAGCATGCGCAGgtgcctcatc ... atgctgacagGAAGAAGAAGGCAGTCCACAAGACCGCAACCACCGATGACAAGCGGCTTCAGAGCACGTTGAAAAGAATTGGAGTGAACACTATTCCTGGTATTGAGGAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 382

ATGAATGTGGAGAAGCTCAAGAAGATGGCGGGTGCTGTGCGCACTGGAGGAAAGGGCAGCATGCGCAGgtgcctcatc ... atgctgacagGAAGAAGAAGGCAGTCCACAAGACCGCAACCACCGATGACAAGCGGCTTCAGAGCACGTTGAAAAGAATTGGAGTGAACACTATTCCTGGTATTGAGGAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 370

ATGAATGTGGAGAAGCTCAAGAAGATGGCGGGTGCTGTGCGCACTGGAGGAAAGGGCAGCATGCGCAGgtgcctcatc ... atgctgacagGAAGAAGAAGGCAGTCCACAAGACCGCAACCACCGATGACAAGCGGCTTCAGAGCACGTTGAAAAGAATTGGAGTGAACACTATTCCTGGTATTGAGGAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 283

ATGAATGTGGAGAAGCTCAAGAAGATGGCGGGTGCTGTGCGCACTGGAGGAAAGGGCAGCATGCGCAGgtgcctcatc ... atgctgacagGAAGAAGAAGGCAGTCCACAAGACCGCAACCACCGATGACAAGCGGCTTCAGAGCACGTTGAAAAGAATTGGAGTGAACACTATTCCTGGTATTGAGGAG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gcttctggacccatagtcccatgctaacaatttatgagggaaaaaatgctgacagGAAGAAGAAGGCAGTCCACAAGACCGCAACCACCGATGACAAGCGGCTTCAGAGCACGTTGAAAAGAATTGGAGTGAACACTATTCCTGGTATTGAGGAG
                     tgctaac  putative branch site (score: 283)
                        taacaatttat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
caccgaagccttttgcgtttgtgatatgatatgttttattgagttgcttctggacccatagtcccatgctaacaatttatgagggaaaaaatgctgacagGAAGAAGAAGGCAGTCCACAAGACCGCAACCACCGATGACAAGCGGCTTCAGAGCACGTTGAAAAGAATTGGAGTGAACACTATTCCTGGTATTGAGGAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGGAG
- - - - -cttttgc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - cccatgc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - gggaaaaa