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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...atagcaatattcttattttttgatgctaagctagcaatggaacacaccttttagctgacagaaagctaacttatgttgtttatattctattctataccagCCGTGTAAAGGAATTTTACTTTTTGGCCCACCTGGTACTGGAAAGACAATGCTTGCTAAGGCTGTGGCAACTGAGGCTGGTGCTAATTTCATAAACATAT

Basic information

species Zea mays
transcript GRMZM2G042074_T02
intron # 16
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G042074_T01 (Zea mays), 3'ss of exon 21
lower sequence: LOC_Os03g22420.1 (Oryza sativa), 3'ss of exon 21
-------atag-caatattcttattttttgatgctaagctagcaatggaacacaccttttagctgacagaaagctaacttatgttgtttatattctattctataccagCCGTGTAAAGGAATTTTACTTTTTGGCCCACCTGGTACTGGAAAGACAATGCTTGCTAAGGCTGTGGCAACTGAGGCTGGTGCTAATTTCATAAACATAT
       || |       |  || |||| |||  |    |     |   |    | |||||  ||| ||  | || |||| |||| ||  |    |||  | | |||||| ||||||||||| |||||||||||||| |||||||| ||||||||||||||||| || |||||||| || ||||||||||| ||||||||||| ||||
gttatgaatggatgggggtactacttttggatagtggaatt----ttttatttccattttatttgatagtgaactgacttttgttattgct----tatgttgtgccagCCATGTAAAGGAATATTACTTTTTGGCCCGCCTGGTACAGGAAAGACAATGCTTGCCAAAGCTGTGGCTACAGAGGCTGGTGCGAATTTCATAAATATAT

upper sequence: GRMZM2G042074_T01 (Zea mays), 3'ss of exon 21
lower sequence: GLYMA10G02410.1 (Glycine max), 3'ss of exon 17
atagcaatattcttattttttgatgctaagctagcaatggaacacaccttttagctgacagaaagctaacttatgt---tgtttatattctattctataccagCCGTGTAAAGGAATTTTACTTTTTGGCCCACCTGGTACTGGAAAGACAATGCTTGCTAAGGCTGTGGCAACTGAGGCTGGTGCTAATTTCATAAACATAT
   | || ||| | |||||       |||   |    || || | |   || ||  ||        |   |   |    |  || || |   ||       |||| || |||||||| || ||||||||||| ||||| || ||||| ||||||||||| |||||||| |||||||| ||||| || ||||| || ||||| |
-gtgaaagattttcattttagttgtttaaatgacttgtgaaagaaattgttgagtagatcatgccatgtgtgtagcacctaattgtaattactttgggtatagCCTTGCAAAGGAATATTGCTTTTTGGCCCTCCTGGCACAGGAAAAACAATGCTTGCAAAGGCTGTAGCAACTGAAGCTGGAGCAAATTTTATTAACATTT

upper sequence: GRMZM2G042074_T01 (Zea mays), 3'ss of exon 21
lower sequence: GLYMA04G37050.1 (Glycine max), 3'ss of exon 4
atagcaatattcttattttttgatgctaagctagcaatggaacacaccttttagctgacagaaagctaacttatgttgt--ttat--attctattctataccagCCGTGTAAAGGAATTTTACTTTTTGGCCCACCTGGTACTGGAAAGACAATGCTTGCTAAGGCTGTGGCAACTGAGGCTGGTGCTAATTTCATAAACATAT
  || || | ||  |    || | | |||  |     || |   |  || ||  |  |     | |    |||| ||||  || |  |||   ||| || | ||||||| || || ||  || | ||||| || ||||| || || |||||||||||||| ||||| || || || || |||||||| |||||||| ||||| |
--agtaaaaatcacaaacattaaag-taatgtgaagttgtaggccttctcttgtcaaattattatcatttttatattgtgattgtgaattgccttccatgc-agCCGTGCAAGGGTATCCTATTATTTGGTCCCCCTGGAACAGGTAAGACAATGCTTGCAAAGGCAGTTGCTACCGAAGCTGGTGCAAATTTCATCAACATTT

upper sequence: GRMZM2G042074_T01 (Zea mays), 3'ss of exon 21
lower sequence: GLYMA10G02400.1 (Glycine max), 3'ss of exon 20
-atagcaatattcttattttttgatgctaagctagcaatggaacacaccttttagctgacagaaagctaacttatgttgtttatattctattcta--tacc--------agCCGTGTAAAGGAATTTTACTTTTTGGCCCACCTGGTACTGGAAAGACAATGCTTGCTAAGGCTGTGGCAACTGAGGCTGGTGCTAATTTCATAAACATAT
  | | |   ||  | |||  |     |||   |  | |||||||||  ||||||  ||  || |   |  | ||||   |   |    ||| ||  |||         |||| || || ||||| || |||||||| || ||||| || ||||| ||||||||||| |||||||| |||||||| ||||| || |||||||| ||||| |
gttggtagattttctttttagttgctttaaatgacaagtggaacacattttttagtagat-gatattcatatcatgtgtgtagcacctcattgtaattactttggatatagCCTTGCAAGGGAATATTGCTTTTTGGGCCCCCTGGCACAGGAAAAACAATGCTTGCAAAGGCTGTAGCAACTGAAGCTGGAGCAAATTTCATTAACATTT

upper sequence: GRMZM2G042074_T01 (Zea mays), 3'ss of exon 21
lower sequence: GLYMA06G17940.1 (Glycine max), 3'ss of exon 21
atagcaatattcttattttttgatgctaagctagcaatggaacacaccttttagctgacagaaagctaactt-atgttgt--ttatattctattctatac-cagCCGTGTAAAGGAATTTTACTTTTTGGCCCACCTGGTACTGGAAAGACAATGCTTGCTAAGGCTGTGGCAACTGAGGCTGGTGCTAATTTCATAAACATAT
   | || | ||  |    || |   |||  |     || | | || || ||  |  |     |   |  || || || |  || |    ||   |  |  |||||||| || || ||  || | ||||| || ||||| || || |||||||||||||| ||||| || || || || |||||||| |||||||| ||||| |
---gtaaaaatcacaaacattaaaa-taatgtgaagttgtagcccatctcttgtcaaattattaatcatttttattttatgattgtgaattaccttccatgcagCCGTGCAAGGGTATCCTATTATTTGGTCCCCCTGGAACAGGTAAGACAATGCTTGCAAAGGCAGTTGCTACCGAAGCTGGTGCAAATTTCATCAACATTT

upper sequence: GRMZM2G042074_T01 (Zea mays), 3'ss of exon 21
lower sequence: GLYMA02G17400.1 (Glycine max), 3'ss of exon 17
-atagcaatattcttattttttgatgctaagctagcaatggaacacaccttt---tagctgacagaaagctaacttatgttgtttatattctattctataccagCCGTGTAAAGGAATTTTACTTTTTGGCCCACCTGGTACTGGAAAGACAATGCTTGCTAAGGCTGTGGCAACTGAGGCTGGTGCTAATTTCATAAACATAT
   |  |||||| | |||||       |||   |    || || |||   ||   ||| | |    | ||          |  || || |   ||       |||| || || ||||| || ||||||||||| ||||| || ||||| ||||||||||| ||||||||||||||||| ||||| || ||||| || ||||| |
gtgaaaaatattttcattttagttgtttaaatgacttgtgaaagacattgttaagtagatcatgccatgcgtgtagcacctaattgtaattactttgggtatagCCTTGCAAGGGAATATTGCTTTTTGGCCCCCCTGGCACAGGAAAAACAATGCTTGCAAAGGCTGTGGCAACTGAAGCTGGAGCAAATTTTATTAACATTT

upper sequence: GRMZM2G042074_T01 (Zea mays), 3'ss of exon 21
lower sequence: GLYMA02G17410.1 (Glycine max), 3'ss of exon 16
-atagcaatattcttattttttgatgctaagctagcaatggaacacaccttttagctgacagaaagctaacttatgttgtttatattctattcta--tacc--------agCCGTGTAAAGGAATTTTACTTTTTGGCCCACCTGGTACTGGAAAGACAATGCTTGCTAAGGCTGTGGCAACTGAGGCTGGTGCTAATTTCATAAACATAT
  |   |   ||  | |||  |     |||   |    |||||||||  ||||||  ||   | |    | | ||||   |   |    ||| ||  |||         |||| || || ||||| || |||||||| || ||||| || ||||| ||||||||||| |||||||| |||||||| ||||| || |||||||| ||||| |
gttgatagattttctttttagttgctttaaatgacttgtggaacacattttttagtagatc-atattcgaatcatgtgtgtagcacctcattgtaattactttggatatagCCTTGCAAGGGAATATTGCTTTTTGGGCCCCCTGGCACAGGAAAAACAATGCTTGCAAAGGCTGTAGCAACTGAAGCTGGAGCAAATTTCATTAACATTT

upper sequence: GRMZM2G042074_T01 (Zea mays), 3'ss of exon 21
lower sequence: GLYMA17G13850.1 (Glycine max), 3'ss of exon 19
atagcaatattcttattttttgatgctaagctagcaatggaacacaccttttagctgacagaaagctaac---ttatgttgtttatattctattctatac-cagCCGTGTAAAGGAATTTTACTTTTTGGCCCACCTGGTACTGGAAAGACAATGCTTGCTAAGGCTGTGGCAACTGAGGCTGGTGCTAATTTCATAAACATAT
    ||||      || |  |     |  | |  | ||  |||   |  |||| |  |     | | |     |||| | |  | |    ||   | |   ||||| || ||||| ||  || | ||||| || ||||| ||||| || ||||||||||| |||||  | || ||||| ||||||||||| ||||| ||||| |
----caattaataaatctaatataattttgatgaccatctaacttgctctttatcaaaatattatccattctgttatctcgactctgaattaccttttgtgcagCCCTGCAAAGGTATCCTATTATTTGGTCCCCCTGGAACTGGTAAAACAATGCTTGCAAAGGCAATTGCTACTGAAGCTGGTGCTAACTTCATCAACATTT

upper sequence: GRMZM2G042074_T01 (Zea mays), 3'ss of exon 21
lower sequence: AT4G02480.1 (Arabidopsis thaliana), 3'ss of exon 20
atagcaatattcttattttttgatgctaagctagcaatggaacacaccttttagctgacagaaagctaacttatgttgtttatattctattctataccagCCGTGTAAAGGAATTTTACTTTTTGGCCCACCTGGTACTGGAAAGACAATGCTTGCTAAGGCTGTGGCAACTGAGGCTGGTGCTAATTTCATAAACATAT
       ||  ||| | ||   || |  |  ||    |         ||  ||  | || |||| | ||| ||| |  || || ||  || |      ||||    ||||| ||  |  | ||||| || ||||||||||||||||| ||||| || || || || |||||||||||||| || |||||||| || || |
------gtac-cttttattgctatacggatttatttgttagttgttactcctacataactgaaaccaaacatatat--ttgatgtttaatgc------agCCTACGAAAGGTATACTGTTGTTTGGACCTCCTGGTACTGGAAAGACGATGCTGGCAAAAGCAGTAGCAACTGAGGCTGGCGCAAATTTCATCAATATCT

upper sequence: GRMZM2G042074_T01 (Zea mays), 3'ss of exon 21
lower sequence: AT4G24860.1 (Arabidopsis thaliana), 3'ss of exon 20
--atagcaatattc--ttattttttgatgctaagctagcaatggaacacaccttttagctgacagaaagctaacttatgttgtttatattctattctataccagCCGTGTAAAGGAATTTTACTTTTTGGCCCACCTGGTACTGGAAAGACAATGCTTGCTAAGGCTGTGGCAACTGAGGCTGGTGCTAATTTCATAAACATAT
   | ||  |  ||  | ||| ||   | ||||  |     | |   ||    |  |  ||   |     ||| | |    | |  | |||   | ||| | |||| |||||||||||| |  | ||||| || ||||| ||||||||||| |||||||| || || |||||||  || |||| ||| || ||||| ||||| |
atttggctttcctcaataattcttctctcctaaaatt-tggtagttaacgttatgca-ttggtggcttcttaa-tcagtccgctcttgttcgtctttatgc-agCCTTGTAAAGGAATTCTTTTATTTGGACCTCCTGGAACTGGAAAGACCATGCTTGCAAAAGCAGTGGCAAAGGAAGCTGATGCGAACTTCATCAACATCT

upper sequence: GRMZM2G042074_T01 (Zea mays), 3'ss of exon 21
lower sequence: AT1G62130.1 (Arabidopsis thaliana), 3'ss of exon 20
---atagcaatattcttattttttgatgctaagctagcaatggaacacaccttttagctgacagaaagctaacttatgttgtttatattctattctataccagCCGTGTAAAGGAATTTTACTTTTTGGCCCACCTGGTACTGGAAAGACAATGCTTGCTAAGGCTGTGGCAACTGAGGCTGGTGCTAATTTCATAAACATAT
    | ||  |  ||  |   |||    |  |  ||     |      || || | | |    |    |  | | |   || |  | | ||  |||| || |||| ||||| |||||| |  | ||||| ||  |||| ||||||||||| |||||||| ||||| |||||||| || |||||||||||  |||| ||||| |
aatttggctttcctcaaaaaatttatctccta--taatttagatgttaacgttatggattggtggcttcctaatcagtctgctcctgtacttctctacac-agCCTTGTAACGGAATTCTCTTATTTGGACCTTCTGGAACTGGAAAGACCATGCTTGCAAAGGCAGTGGCAACGGAAGCTGGTGCTAACCTCATCAACATGT

upper sequence: GRMZM2G042074_T01 (Zea mays), 3'ss of exon 21
lower sequence: Vv07s0005g00200.t01 (Vitis vinifera), 3'ss of exon 20
------------------------------------------atagcaatattct-tattttttgatgctaagct---agcaatggaacacaccttttagctgacagaaagctaacttat--gttgtttatatt---ctattctataccagCCGTGTAAAGGAATTTTACTTTTTGGCCCACCTGGTACTGGAAAGACAATGCTTGCTAAGGCTGTGGCAACTGAGGCTGGTGCTAATTTCATAAACATAT
                                          |||   ||||| | ||| |  ||    |    |   |   ||||||   |  ||||| || |   |   ||    | |   |  | |  ||     || | | |  ||||| || || |||||| | || ||||| || ||||| |||||||| ||||||||||| ||||| || ||||||||||| ||||| ||||| || |||||||
gttaggtgtttcacatgttttatttctttattgtgtatgtatatatatatattgtgtatctggtggaattttcttttgaattatggaa-gtaagttttatctaattcatgccttgtatgtctatcatctgaatgaggttactatttttcagCCTTGCAAGGGAATTCTTCTATTTGGGCCTCCTGGGACTGGAAAAACAATGCTTGCGAAGGCGGTTGCAACTGAGGCAGGTGCAAATTTTATCAACATAT

upper sequence: GRMZM2G042074_T01 (Zea mays), 3'ss of exon 21
lower sequence: Vv17s0000g01550.t01 (Vitis vinifera), 3'ss of exon 21
------atagcaatattcttattttttgatgctaagctagcaatggaacacaccttttagctgacagaaagctaacttatgttgtttatattctattctataccagCCGTGTAAAGGAATTTTACTTTTTGGCCCACCTGGTACTGGAAAGACAATGCTTGCTAAGGCTGTGGCAACTGAGGCTGGTGCTAATTTCATAAACATAT
      ||     |   |  |    || |         ||| || || |    |  ||   |   |   | | | ||||   |||   | ||| ||       ||||| || || || ||  | || |||||||| ||||| || || ||||||||||||||||||||||| || ||||| |||||||| || ||||| || || |
cagttcatcaggctgaacagagcacttcaaatactatcagctattgatctttgcaattgtgttctaaggaacaatctta--gtgtaattgttccatgtg----cagCCTTGCAAGGGCATACTTCTATTTGGCCCCCCTGGAACAGGCAAGACAATGCTTGCTAAGGCTGTTGCTACTGAAGCTGGTGCAAACTTCATCAATATTT

upper sequence: GRMZM2G042074_T01 (Zea mays), 3'ss of exon 21
lower sequence: PP1S3_184V6.1 (Physcomitrella patens), 3'ss of exon 17
----atagcaatattcttattttttgatgctaagctagcaatgg-aacacaccttttagctgacagaaagctaacttatgt-tgtttatattctattctataccagCCGTGTAAAGGAATTTTACTTTTTGGCCCACCTGGTACTGGAAAGACAATGCTTGCTAAGGCTGTGGCAACTGAGGCTGGTGCTAATTTCATAAACATAT
    || | |  ||| |||||  || ||  ||   |  | ||    |  |   ||     |   |  |   | |   |||    | | |  ||| || | | | |||| || | |||  |||| || ||||| ||||| ||||| || ||||| ||| | ||||||||||| |||||||| || || ||||| ||||||||||| |
ggctattggatgatttttattcgtttat-ttattttgacgattatgatgcgtattaatattattattattttga---atgcacatctcttctctgtt-tgtgc-agCCATGCAGAGGCCTTTTGCTATTTGGACCACCAGGTACAGGGAAGACTATGTTAGCTAAGGCTGTTGCAACTGAAGCAGGGGCTAACTTCATAAACATTT

upper sequence: GRMZM2G042074_T01 (Zea mays), 3'ss of exon 21
lower sequence: EFJ31084 (Selaginella moellendorffii), 3'ss of exon 8
atagcaatattcttattttttgatgctaagctagcaatggaacacaccttttagctgacagaaagctaacttatgttgtttatattctattctataccagCCGTGTAAAGGAATTTTACTTTTTGGCCCACCTGGTACTGGAAAGACAATGCTTGCTAAGGCTGTGGCAACTGAGGCTGGTGCTAATTTCATAAACATAT
                                               || |  | |        |||   ||   |||| || |     || |||  ||||| ||||  ||  |  |  | ||||| || || || ||||| ||||| |||||||||||||| || || || ||||||||||| |||||||| || || |
---------------------------------------------gtctgtgtgtttgttatttgctttttttctttgtcta-acgaatttatatggcagCCTTGTAGGGGCCTACTCTTATTTGGTCCTCCAGGAACTGGTAAGACCATGCTTGCTAAGGCGGTTGCTACAGAGGCTGGTGCAAATTTCATCAATATTT

upper sequence: GRMZM2G042074_T01 (Zea mays), 3'ss of exon 21
lower sequence: EFJ34631 (Selaginella moellendorffii), 3'ss of exon 10
atagcaatattcttattttttgatgctaagctagcaatggaacacaccttttagctgacagaaagctaacttatgttgtttatattctattctataccagCCGTGTAAAGGAATTTTACTTTTTGGCCCACCTGGTACTGGAAAGACAATGCTTGCTAAGGCTGTGGCAACTGAGGCTGGTGCTAATTTCATAAACATAT
                                               || |  | |        |||   ||   |||| || |      | |||  ||||| ||||  ||  |  |  | ||||| || || || ||||| ||||| |||||||||||||| || || || ||||||||||| |||||||| || || |
---------------------------------------------gtctgtgtgtttgttatttgctttttttctttgtcta-acgaatctatatggcagCCTTGTAGGGGCCTACTCTTATTTGGTCCTCCAGGAACTGGTAAGACCATGCTTGCTAAGGCGGTTGCTACAGAGGCTGGTGCAAATTTCATCAATATTT

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|67017525|gb|CO446274.1|CO446274
EST:     TGCTTCCTTTGCAAAGACCTGAACTTTTTAACCGAGGACAACTTATGAAG                         CCGTGTAAAGGAATTTTACTTTTTGGCCCACCTGGTACTGGAAAGACAATG
genomic: TGCTTCCTTTGCAAAGACCTGAACTTTTTAACCGAGGACAACTTATGAAGgtatatttca ... tctataccagCCGTGTAAAGGAATTTTACTTTTTGGCCCACCTGGTACTGGAAAGACAATG
EST: gi|31359802|gb|CD444159.1|CD444159
EST:     TGCTTCCTTTGCAAAGACCTGAACTTTTTAACCGAGGACAACTTATGAAG                         CCGTGTAAAGGAATTTTACTTTTTGGCCCACCTGGTACTGGAAAGACAATG
genomic: TGCTTCCTTTGCAAAGACCTGAACTTTTTAACCGAGGACAACTTATGAAGgtatatttca ... tctataccagCCGTGTAAAGGAATTTTACTTTTTGGCCCACCTGGTACTGGAAAGACAATG

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: 48 (upstream exon), 49 (downstream exon)
Score: 177

GGACATTGGAGCTTTAGAAAGTGTCAAAGATACTCTGAAGGAGTTAGTGATGCTTCCTTTGCAAAGACCTGAACTTTTTAACCGAGGACAACTTATGAAGgtatatttca ... tctataccagCCGTGTAAAGGAATTTTACTTTTTGGCCCACCTGGTACTGGAAAGACAATGCTTGCTAAGGCTGTGGCAACTGAGGCTGGTGCTAATTTCATAAACATAT


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 216

GGACATTGGAGCTTTAGAAAGTGTCAAAGATACTCTGAAGGAGTTAGTGATGCTTCCTTTGCAAAGACCTGAACTTTTTAACCGAGGACAACTTATGAAGgtatatttca ... tctataccagCCGTGTAAAGGAATTTTACTTTTTGGCCCACCTGGTACTGGAAAGACAATGCTTGCTAAGGCTGTGGCAACTGAGGCTGGTGCTAATTTCATAAACATAT


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 173

GGACATTGGAGCTTTAGAAAGTGTCAAAGATACTCTGAAGGAGTTAGTGATGCTTCCTTTGCAAAGACCTGAACTTTTTAACCGAGGACAACTTATGAAGgtatatttca ... tctataccagCCGTGTAAAGGAATTTTACTTTTTGGCCCACCTGGTACTGGAAAGACAATGCTTGCTAAGGCTGTGGCAACTGAGGCTGGTGCTAATTTCATAAACATAT


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 295

GGACATTGGAGCTTTAGAAAGTGTCAAAGATACTCTGAAGGAGTTAGTGATGCTTCCTTTGCAAAGACCTGAACTTTTTAACCGAGGACAACTTATGAAGgtatatttca ... tctataccagCCGTGTAAAGGAATTTTACTTTTTGGCCCACCTGGTACTGGAAAGACAATGCTTGCTAAGGCTGTGGCAACTGAGGCTGGTGCTAATTTCATAAACATAT




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

accttttagctgacagaaagctaacttatgttgtttatattctattctataccagCCGTGTAAAGGAATTTTACTTTTTGGCCCACCTGGTACTGGAAAGACAATGCTTGCTAAGGCTGTGGCAACTGAGGCTGGTGCTAATTTCATAAACATAT
                  agctaac  putative branch site (score: 295)
                                       ttctattct  putative PPT
                         ttatgttgtttatatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
atagcaatattcttattttttgatgctaagctagcaatggaacacaccttttagctgacagaaagctaacttatgttgtttatattctattctataccagCCGTGTAAAGGAATTTTACTTTTTGGCCCACCTGGTACTGGAAAGACAATGCTTGCTAAGGCTGTGGCAACTGAGGCTGGTGCTAATTTCATAAACATAT

- - - - - - - - - - tgatgct
- - - - - - - - - - - - - - - - - - - - - - - - - - -gctgaca
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tgttgtt