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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...caatatttttttctccttattcattctttgtattgtcaagaaggttcttatacaacctttaacgttgttttgtctctattgtgcccgtgtacatccacagGGGTATGGAACTCTGTTAATGGAAGAAGCAGAAAGGATTGCTCAAAAGGAGCACCGTTCAGAGAAATTGGCTGTCATTTCGGGGGTTGGTACTCGCCACT

Basic information

species Zea mays
transcript GRMZM2G100872_T01
intron # 8
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G100872_T01 (Zea mays), 3'ss of exon 8
lower sequence: LOC_Os04g40840.1 (Oryza sativa), 3'ss of exon 8
--caatatttttttctccttattcattctttgtattgtcaagaaggttcttatacaacctttaacgttgttttgtctctattgtgcccgtgtacatccacagGGGTATGGAACTCTGTTAATGGAAGAAGCAGAAAGGATTGCTCAAAAGGAGCACCGTTCAGAGAAATTGGCTGTCATTTCGGGGGTTGGTACTCGCCACT
   | |     ||  | | |    ||   |    ||   ||   | || |     ||  |  |      || ||  | | || || |  |  ||||| |||||| ||||| ||||| || ||||||||||||||||| |||||||  |||||||| |||||| ||||| | ||||| || || || ||||| ||||||||||
ttgacttgcaattggtacatgcctatagatatacttcctaacttgattgtccagaaatataaattacatttctgatttttttttgac--tcaacatcgacagGGTTATGGTACTCTTTTGATGGAAGAAGCAGAAAGAATTGCTCGCAAGGAGCATCGTTCAAAGAAAATCGCTGTTATATCAGGAGTTGGGACTCGCCACT

upper sequence: GRMZM2G100872_T01 (Zea mays), 3'ss of exon 8
lower sequence: EFJ27084 (Selaginella moellendorffii), 3'ss of exon 5
----------caatatttttttctccttattcattctttgtattgtcaagaaggttc--ttatacaacc-tttaacgttgttttgtctctattgtgcccgtgtacatcca-------cagGGGTATGGAACTCTGTTAATGGAAGAAGCAGAAAGGATTGCTCAAAAGGAGCACCGTTCAGAGAAATTGGCTGTCATTTCGGGGGTTGGTACTCGCCACT
           |      | |  | |   |||||     ||   | | | ||| | |      |   |  |||    |  | ||    |||||||  |    ||| ||||       ||||| ||||||||||| || ||||||||||| || ||||| ||||  |||||||| || || | |||| |||| || || ||                    
gctgcacgtttatggaactgtggtgccggttcatggcc-gtgacgccgacaagctacaacaccatgtctatttgttttcatctttatcctattgtctcaagCTACTTCCAATTTGTACAGGGTTATGGAACTCTTTTGATGGAAGAAGCCGAGAGGATAGCTCGCAAGGAGCATCGATCCGTGAAACTGGCAGTGATATCC-------------------

upper sequence: GRMZM2G100872_T01 (Zea mays), 3'ss of exon 8
lower sequence: EFJ27078 (Selaginella moellendorffii), 3'ss of exon 8
caatatttttttctccttattcattctttgtattgtcaagaaggttcttatacaacctttaacgttgttttgtctctattgtgcccgtgtacatccacagGGGTATGGAACTCTGTTAATGGAAGAAGCAGAAAGGATTGCTCAAAAGGAGCACCGTTCAGAGAAATTGGCTGTCATTTCGGGGGTTGGTACTCGCCACT
                                           ||   | |     | |     |  | ||||||| |   | |      |  |  |||||| ||||||||||| || ||||||||||| || ||||| ||||  |||||||| || || | |||| |||| || || || || || || ||| | ||||
-------------------------------------------gtctatttgttttcatctttatcctattgtctcaagc-tacttccaaat-tgtacagGGTTATGGAACTCTTTTGATGGAAGAAGCCGAGAGGATAGCTCGCAAGGAGCATCGATCCGTGAAACTGGCAGTGATATCCGGAGTGGGAACTAGACACT

upper sequence: GRMZM2G100872_T01 (Zea mays), 3'ss of exon 8
lower sequence: EFJ21486 (Selaginella moellendorffii), 3'ss of exon 8
caatatttttttctccttattcattctttgtattgtcaagaaggttcttatacaacctttaacgttgttttgtctctattgtgcccgtgtacatccacagGGGTATGGAACTCTGTTAATGGAAGAAGCAGAAAGGATTGCTCAAAAGGAGCACCGTTCAGAGAAATTGGCTGTCATTTCGGGGGTTGGTACTCGCCACT
                                           |||  | |     | |     |  | ||||||| |  |   |     |  |  |||||| ||||||||||| |||||||||||||| || ||||| |||| ||||||||| || || | |||| |||| || || ||||| || || ||| | ||||
-------------------------------------------gtttatttgttttcatctttatcctattgtctcaa--gctacttccaatttgtacagGGTTATGGAACTCTTTTAATGGAAGAAGCCGAGAGGATAGCTCGAAAGGAGCATCGATCCGTGAAACTGGCAGTGATATCGGGAGTGGGAACTAGACACT

upper sequence: GRMZM2G100872_T01 (Zea mays), 3'ss of exon 8
lower sequence: EFJ21495 (Selaginella moellendorffii), 3'ss of exon 6
caatatttttttctccttattcattctttgtattgtcaagaaggttcttatacaacctttaacgttgttttgtctctattgtgcccgtgtacatccacagGGGTATGGAACTCTGTTAATGGAAGAAGCAGAAAGGATTGCTCAAAAGGAGCACCGTTCAGAGAAATTGGCTGTCATTTCGGGGGTTGGTACTCGCCACT
                                           ||   | |     | |     |  | ||||||| |  |   |     |  |  |||||| ||||||||||| || ||||||||||| || ||||| ||||  |||||||| || || | |||| |||| || || || || || || ||| | ||||
-------------------------------------------gtctatttgttttcatctttatcctattgtctcaa--gctacttccaatttgtacagGGTTATGGAACTCTTTTGATGGAAGAAGCCGAGAGGATAGCTCGCAAGGAGCATCGATCCGTGAAACTGGCAGTGATATCCGGAGTGGGAACTAGACACT

upper sequence: GRMZM2G100872_T01 (Zea mays), 3'ss of exon 8
lower sequence: EFJ27096 (Selaginella moellendorffii), 3'ss of exon 7
caatatttttttctccttattcattctttgtattgtca-agaaggttcttatacaacctttaacgttgttttgtctctattgtgcccgtgtacatccacagGGGTATGGAACTCTGTTAATGGAAGAAGCAGAAAGGATTGCTCAAAAGGAGCACCGTTCAGAGAAATTGGCTGTCATTTCGGGGGTTGGTACTCGCCACT
   |   | ||        |     |       | | | |  ||||   | |     | |     |  | ||||||| |  |   |     |  |  |||||| ||||||||||| || ||||||||||| || ||||| ||||  |||||||| || || | |||| |||| || || || || || || ||| | ||||
--gtgcctgttcacggccgtgacgccgacaagctataacaccaggtctatttgttttcatctttatcctattgtctcaa--gctacttccaatttgtacagGGTTATGGAACTCTTTTGATGGAAGAAGCCGAGAGGATAGCTCGCAAGGAGCATCGATCCGTGAAACTGGCAGTGATATCCGGAGTGGGAACTAGACACT

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|166457698|gb|EG159070.1|EG159070
EST:     CCGTGATGTAGACAAGCTACAGCACCAG                         GGGTATGGAACTCTGTTAATGGAAGAAGCAGAAAGGATTGCTCAAAAGGAG
genomic: CCGTGATGTAGACAAGCTACAGCACCAGgtgattcact ... acatccacagGGGTATGGAACTCTGTTAATGGAAGAAGCAGAAAGGATTGCTCAAAAGGAG
EST: gi|78121953|gb|DV540337.1|DV540337
EST:     GAACTGCAGTCCCTGTGCATGGCCGTGATGTAGACAAGCTACAGCACCAG                         GGGTATGGAACTCTGTTAATGGAAGAAGCAGAAAGGATTGCTCAAAAGGAG
genomic: GAACTGCAGTCCCTGTGCATGGCCGTGATGTAGACAAGCTACAGCACCAGgtgattcact ... acatccacagGGGTATGGAACTCTGTTAATGGAAGAAGCAGAAAGGATTGCTCAAAAGGAG
EST: gi|76923550|gb|DV169542.1|DV169542
EST:     GAACTGCAGTCCCTGTGCATGGCCGTGATGTAGACAAGCTACAGCCCCAG                         GGGTATGGAACTCTGTTAATGGAAGAAGCAGAAAGGATTGCTCAAAAGGAG
genomic: GAACTGCAGTCCCTGTGCATGGCCGTGATGTAGACAAGCTACAGCACCAGgtgattcact ... acatccacagGGGTATGGAACTCTGTTAATGGAAGAAGCAGAAAGGATTGCTCAAAAGGAG
EST: gi|6654212|gb|AW267617.1|AW267617
EST:     GAACTGCAGTCCCTGTGCATGGCCGTGATGTAGACAAGCTACAGCACCAG                         GGGTATGGAACTCTGTTAATGGAAGAAGCAGAAAGGATTGCTCAAAAGGAG
genomic: GAACTGCAGTCCCTGTGCATGGCCGTGATGTAGACAAGCTACAGCACCAGgtgattcact ... acatccacagGGGTATGGAACTCTGTTAATGGAAGAAGCAGAAAGGATTGCTCAAAAGGAG
EST: gi|101399515|gb|EB821625.1|EB821625
EST:     GAACTGCAGTCCCTGTGCATGGCCGTGATGTAGACAAGCTACAGCACCAG                         GGGTATGGAACTCTGTTAATGGAAGAAGCAGAAAGGATTGCTCAAAAGGAG
genomic: GAACTGCAGTCCCTGTGCATGGCCGTGATGTAGACAAGCTACAGCACCAGgtgattcact ... acatccacagGGGTATGGAACTCTGTTAATGGAAGAAGCAGAAAGGATTGCTCAAAAGGAG
EST: gi|67025678|gb|CO454427.1|CO454427
EST:     GAACTGCAGTCCCTGTGCATGGCCGTGATGTAGACAAGCTACAGCACCAA                         GGGTATGGAACTCTGTTAATGGAAGAAGCAGAAAGGATTGCTCAAAAAGAG
genomic: GAACTGCAGTCCCTGTGCATGGCCGTGATGTAGACAAGCTACAGCACCAGgtgattcact ... acatccacagGGGTATGGAACTCTGTTAATGGAAGAAGCAGAAAGGATTGCTCAAAAGGAG
EST: gi|211184732|gb|FL162030.1|FL162030
EST:     GAACTGCAGTCCCTGTGCATGGCCGTGATGTAGACAAGCTACAGCACCAG                         GGGTATGGAACTCTGTTAATGGAAGAAGCAGAAAGGATTGCTCAAAAGGAG
genomic: GAACTGCAGTCCCTGTGCATGGCCGTGATGTAGACAAGCTACAGCACCAGgtgattcact ... acatccacagGGGTATGGAACTCTGTTAATGGAAGAAGCAGAAAGGATTGCTCAAAAGGAG
EST: gi|91049794|gb|EB160212.1|EB160212
EST:     GAACTGCAGTCCCTGTGCATGGCCGTGATGTAGACAAGCTACAGCACCAG                         GGGTATGGAACTCTGTTAATGGAAGAAGCAGAAAGGATTGCTCAAAAGGAG
genomic: GAACTGCAGTCCCTGTGCATGGCCGTGATGTAGACAAGCTACAGCACCAGgtgattcact ... acatccacagGGGTATGGAACTCTGTTAATGGAAGAAGCAGAAAGGATTGCTCAAAAGGAG
EST: gi|32864279|gb|CF003961.1|CF003961
EST:     GAACTGCAGTCCCTGTGCATGGCCGTGATGTAGACAAGCTACAGCACCAG                         GGGTATGGAACTCTGTTAATGGAAGAATCAGAAAGGATTGCTCAAAAGGAG
genomic: GAACTGCAGTCCCTGTGCATGGCCGTGATGTAGACAAGCTACAGCACCAGgtgattcact ... acatccacagGGGTATGGAACTCTGTTAATGGAAGAAGCAGAAAGGATTGCTCAAAAGGAG
EST: gi|20337000|gb|BQ172630.1|BQ172630
EST:     GAACTGCAGTCCCTGTGCATGGCCGTGATGTAGACAAGCTACAGCACCAG                         GGGTATGGAACTCTGTTAATGGAAGAAGCAGAAAGGATTGCTCAAAAGGAG
genomic: GAACTGCAGTCCCTGTGCATGGCCGTGATGTAGACAAGCTACAGCACCAGgtgattcact ... acatccacagGGGTATGGAACTCTGTTAATGGAAGAAGCAGAAAGGATTGCTCAAAAGGAG

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: 47 (upstream exon), 47 (downstream exon)
Score: 65

CCCTGAACTTGTAGGGAGGTGTTCAATTGTTCGTGAGCTTCATGTCTATGGAACTGCAGTCCCTGTGCATGGCCGTGATGTAGACAAGCTACAGCACCAGgtgattcact ... acatccacagGGGTATGGAACTCTGTTAATGGAAGAAGCAGAAAGGATTGCTCAAAAGGAGCACCGTTCAGAGAAATTGGCTGTCATTTCGGGGGTTGGTACTCGCCACT


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 54

CCCTGAACTTGTAGGGAGGTGTTCAATTGTTCGTGAGCTTCATGTCTATGGAACTGCAGTCCCTGTGCATGGCCGTGATGTAGACAAGCTACAGCACCAGgtgattcact ... acatccacagGGGTATGGAACTCTGTTAATGGAAGAAGCAGAAAGGATTGCTCAAAAGGAGCACCGTTCAGAGAAATTGGCTGTCATTTCGGGGGTTGGTACTCGCCACT


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 82

CCCTGAACTTGTAGGGAGGTGTTCAATTGTTCGTGAGCTTCATGTCTATGGAACTGCAGTCCCTGTGCATGGCCGTGATGTAGACAAGCTACAGCACCAGgtgattcact ... acatccacagGGGTATGGAACTCTGTTAATGGAAGAAGCAGAAAGGATTGCTCAAAAGGAGCACCGTTCAGAGAAATTGGCTGTCATTTCGGGGGTTGGTACTCGCCACT


Block sizes: 48 (upstream exon), 47 (downstream exon)
Score: 45

CCCTGAACTTGTAGGGAGGTGTTCAATTGTTCGTGAGCTTCATGTCTATGGAACTGCAGTCCCTGTGCATGGCCGTGATGTAGACAAGCTACAGCACCAGgtgattcact ... acatccacagGGGTATGGAACTCTGTTAATGGAAGAAGCAGAAAGGATTGCTCAAAAGGAGCACCGTTCAGAGAAATTGGCTGTCATTTCGGGGGTTGGTACTCGCCACT




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tcttatacaacctttaacgttgttttgtctctattgtgcccgtgtacatccacagGGGTATGGAACTCTGTTAATGGAAGAAGCAGAAAGGATTGCTCAAAAGGAGCACCGTTCAGAGAAATTGGCTGTCATTTCGGGGGTTGGTACTCGCCACT
           ctttaac  putative branch site (score: 45)
                   ttgtttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
caatatttttttctccttattcattctttgtattgtcaagaaggttcttatacaacctttaacgttgttttgtctctattgtgcccgtgtacatccacagGGGTATGGAACTCTGTTAATGGAAGAAGCAGAAAGGATTGCTCAAAAGGAGCACCGTTCAGAGAAATTGGCTGTCATTTCGGGGGTTGGTACTCGCCACT

- - - - - - - - - - - - - - tgtattg
- - - - - - - - - - - - - - - - - - - - - - - - -atacaac