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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagtgacagtgctcaactgataatctaatttcatgatatataacatcagaactaattgtttatacacatacagTTCACCCCCCATCCACATGCTGGCGACAAGTGGTGTGTCTATCCGAGCTATGACTACGCTCATTGCATGGTGGATTCTCTTGAAAACATCACACATTCG

Basic information

species Zea mays
transcript GRMZM2G032049_T01
intron # 12
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G032049_T01 (Zea mays), 3'ss of exon 12
lower sequence: LOC_Os01g09000.1 (Oryza sativa), 3'ss of exon 12
gtaagtgacagtgctcaactgataatctaatttcatgatat---ataacatcagaactaattgttt-atacacatacagTTCACCCCCCATCCACATGCTGGCGACAAGTGGTGTGTCTATCCGAGCTATGACTACGCTCATTGCATGGTGGATTCTCTTGAAAACATCACACATTCG
|||||  |     || || || |  | |  ||   |  |     ||||   || |||| |   | | ||   |||||||||||| || |||||||||||||| || ||||||||  ||||||| ||||||||||| ||||| |||||||||||||||||||| ||||| |||||||||
gtaagcaatgcaactgaattg-tgttttgcttgtctatttcctgataaatacacaactcacactctgatgaccatacagTTCACTCCTCATCCACATGCTGGTGATAAGTGGTGCATCTATCCAAGCTATGACTATGCTCACTGCATGGTGGATTCTCTTGAGAACATTACACATTCG

upper sequence: GRMZM2G032049_T01 (Zea mays), 3'ss of exon 12
lower sequence: GLYMA20G25120.2 (Glycine max), 3'ss of exon 13
----gtaagtgacagtgctcaactgataatctaatttc-----------atgatatataacatcagaactaattg-tttatacacatacagTTCACCCCCCATCCACATGCTGGCGACAAGTGGTGTGTCTATCCGAGCTATGACTACGCTCATTGCATGGTGGATTCTCTTGAAAACATCACACATTCG
    |||    || |   |    |  |  || ||||||           || || |||  | |  ||  | | || ||| | ||  |  |||| ||||| || || |||||||| ||||| |||||| ||||||| || ||||| || || || ||||| ||||||||||| || || ||||||||||| 
gtaagtactcaactgcatttttttattgctcaaatttctttgggagataataatttatttcttatgacgtgaatgctttctgcatct-tagTTTACCCCACACCCTCATGCTGGAGACAAATGGTGTATCTATCCAAGTTATGATTATGCACACTGCATTGTGGATTCTCTAGAGAATATCACACATTCA

upper sequence: GRMZM2G032049_T01 (Zea mays), 3'ss of exon 12
lower sequence: GLYMA10G41920.2 (Glycine max), 3'ss of exon 13
----gtaagtgacagtgctcaactgataatctaatttcatgatatataacatcagaact-----------aattgtttatacacatacagTTCACCCCCCATCCACATGCTGGCGACAAGTGGTGTGTCTATCCGAGCTATGACTACGCTCATTGCATGGTGGATTCTCTTGAAAACATCACACATTCG
    |||    ||     |    |  |  || ||||||  |  | ||||     ||  |           |||  ||| | ||  |  |||| ||||| || || |||||||| ||||| |||||| ||||||| || ||||| || || |||||||| ||||||||||| || || ||||||||||| 
gcaagtactcaactacatttttttattgctcaaatttctaggaagataatgattgatttcttatgatgtgaatgctttctgcat-tttagTTTACCCCACACCCTCATGCTGGAGACAAATGGTGTATCTATCCAAGTTATGATTATGCACATTGCATTGTGGATTCTCTAGAGAATATCACACATTCT

upper sequence: GRMZM2G032049_T01 (Zea mays), 3'ss of exon 12
lower sequence: AT1G25350.2 (Arabidopsis thaliana), 3'ss of exon 13
gtaagtgacagtg-------ctcaactgataatctaatttcatgatatataacatcagaact------aattgtttatacacat-acagTTCACCCCCCATCCACATGCTGGCGACAAGTGGTGTGTCTATCCGAGCTATGACTACGCTCATTGCATGGTGGATTCTCTTGAAAACATCACACATTCG
| |||||| | |        ||| | | | |    ||    | | | | |  | ||    |       | ||||| |||  | |  |||||| | || |||||  | ||||| |||||||||||| |||||||||| ||||| || || || ||||  || ||||||||||| || || || ||||||
gcaagtgaaactaaaatcctctctagttacatataaaaagtaggctctctctcttcttttcctgtctgacttgttaatatgctttgcagTTCGCACCTCATCCTAAGGCTGGTGACAAGTGGTGTATCTATCCGAGTTATGATTATGCCCACTGCACTGTTGATTCTCTTGAGAATATAACGCATTCG

upper sequence: GRMZM2G032049_T01 (Zea mays), 3'ss of exon 12
lower sequence: Vv15s0021g01230.t01 (Vitis vinifera), 3'ss of exon 13
-------------------------------gtaagtgacagtgctcaactgataatctaatttcatgatatataacatcagaa----ctaattgtttatacac-----atacagTTCACCCCCCATCCACATGCTGGCGACAAGTGGTGTGTCTATCCGAGCTATGACTACGCTCATTGCATGGTGGATTCTCTTGAAAACATCACACATTCG
                                | |     |||  | |    || | ||| |   |  | | | ||||| || |    ||||||| ||  ||        | ||||| || || || ||||||||||| |||||||||||||| ||||| || || || || ||||||||||| || ||||||||||| |||||||| ||||| 
gcaagtctgtactcatagacatcttaactatttcaacatgagtagttactaaattaccta-tcaaaaaaaaaaaaacatgagtagttactaattgatttcacttcttttgtccagTTTACTCCTCACCCACATGCTGGAGACAAGTGGTGTGTTTATCCAAGTTACGATTATGCTCATTGCATTGTAGATTCTCTTGAGAACATCACTCATTCA

upper sequence: GRMZM2G032049_T01 (Zea mays), 3'ss of exon 12
lower sequence: Vv01s0011g03740.t01 (Vitis vinifera), 3'ss of exon 13
gtaagtgacagtgctcaactg----ataatctaatttcatgatata-----taacatcagaacta---attgtttatacacatacagTTCACCCCCCATCCACATGCTGGCGACAAGTGGTGTGTCTATCCGAGCTATGACTACGCTCATTGCATGGTGGATTCTCTTGAAAACATCACACATTCG
| |||||  |    |  |        ||    |  |||| | ||       | |    ||   |    ||| ||  ||  | | ||||| ||||| ||||||||| | || |||||||||||| | ||||| || ||||| ||  |||||||||| ||||||||||||||||| || |||||||||
gcaagtgctaacctttgaacatgttgtagctcacattcaaggtactactctttattcaagggtttgacatttttgttattcgtccagTTTACCCCTCATCCACATTCAGGGGACAAGTGGTGTATTTATCCAAGTTATGATTATTCTCATTGCATTGTGGATTCTCTTGAAAATATTACACATTCG

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|32933496|gb|CF038308.1|CF038308
EST:     TGCAAAATGAGAACAAAAATATGTCTGACTTAATAGCATATAGAATAAAA                         TTCACCCCCCATCCACATGCTGGTGACAAGTGGTGTGTCTATCCGAGCTAT
genomic: TGCAAAATGAGAACAAAAATATGTCTGACTTAATAGCATATAGAATAAAAgtaagtgaca ... acacatacagTTCACCCCCCATCCACATGCTGGCGACAAGTGGTGTGTCTATCCGAGCTAT
EST: gi|32934107|gb|CF038919.1|CF038919
EST:     TGCAAAATGAGAACAAAAATATGTCTGACTTAATAGCATATAGAATAAAA                         TTCACCCCCCATCCACATGCTGGTGACAAGTGGTGTGTCTATCCGAGCTAT
genomic: TGCAAAATGAGAACAAAAATATGTCTGACTTAATAGCATATAGAATAAAAgtaagtgaca ... acacatacagTTCACCCCCCATCCACATGCTGGCGACAAGTGGTGTGTCTATCCGAGCTAT
EST: gi|32933499|gb|CF038311.1|CF038311
EST:     TGCAAAATGAGAACAAAAATATGTCTGACTTAATAGCATGTAGAATAAAA                         TTCACCCCCCATCCACATGCTGGTGACAAGTGGTGTGTCTATCCGAGCTAT
genomic: TGCAAAATGAGAACAAAAATATGTCTGACTTAATAGCATATAGAATAAAAgtaagtgaca ... acacatacagTTCACCCCCCATCCACATGCTGGCGACAAGTGGTGTGTCTATCCGAGCTAT

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: 185

GCGTGGGTTGATTGCAGAGGGTGCAGCAACTCTCCGTATGAAGCAGGATATGCAAAATGAGAACAAAAATATGTCTGACTTAATAGCATATAGAATAAAAgtaagtgaca ... acacatacagTTCACCCCCCATCCACATGCTGGCGACAAGTGGTGTGTCTATCCGAGCTATGACTACGCTCATTGCATGGTGGATTCTCTTGAAAACATCACACATTCG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 149

GCGTGGGTTGATTGCAGAGGGTGCAGCAACTCTCCGTATGAAGCAGGATATGCAAAATGAGAACAAAAATATGTCTGACTTAATAGCATATAGAATAAAAgtaagtgaca ... acacatacagTTCACCCCCCATCCACATGCTGGCGACAAGTGGTGTGTCTATCCGAGCTATGACTACGCTCATTGCATGGTGGATTCTCTTGAAAACATCACACATTCG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 245

GCGTGGGTTGATTGCAGAGGGTGCAGCAACTCTCCGTATGAAGCAGGATATGCAAAATGAGAACAAAAATATGTCTGACTTAATAGCATATAGAATAAAAgtaagtgaca ... acacatacagTTCACCCCCCATCCACATGCTGGCGACAAGTGGTGTGTCTATCCGAGCTATGACTACGCTCATTGCATGGTGGATTCTCTTGAAAACATCACACATTCG


Block sizes: 49 (upstream exon), 47 (downstream exon)
Score: 166

GCGTGGGTTGATTGCAGAGGGTGCAGCAACTCTCCGTATGAAGCAGGATATGCAAAATGAGAACAAAAATATGTCTGACTTAATAGCATATAGAATAAAAgtaagtgaca ... acacatacagTTCACCCCCCATCCACATGCTGGCGACAAGTGGTGTGTCTATCCGAGCTATGACTACGCTCATTGCATGGTGGATTCTCTTGAAAACATCACACATTCG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gataatctaatttcatgatatataacatcagaactaattgtttatacacatacagTTCACCCCCCATCCACATGCTGGCGACAAGTGGTGTGTCTATCCGAGCTATGACTACGCTCATTGCATGGTGGATTCTCTTGAAAACATCACACATTCG
                               aactaat  putative branch site (score: 166)
       taatttcatgatatat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaagtgacagtgctcaactgataatctaatttcatgatatataacatcagaactaattgtttatacacatacagTTCACCCCCCATCCACATGCTGGCGACAAGTGGTGTGTCTATCCGAGCTATGACTACGCTCATTGCATGGTGGATTCTCTTGAAAACATCACACATTCG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGTGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGTGGA