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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...atgatatgggtgcctctgtccatctgtcagttgtatctctgcttgtcgctgttcggtgtggagtttctgttaacaatcatattgtacctttttcccgcagGAATTACAATTGCCGAGTATTTTCGTGATATGGGCTACAACGTTAGTATGATGGCTGACTCCACCTCACGATGGGCTGAGGCTTTGCGTGAGATCTCAGG

Basic information

species Zea mays
transcript GRMZM2G128877_T03
intron # 8
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G128877_T03 (Zea mays), 3'ss of exon 8
lower sequence: LOC_Os02g07870.1 (Oryza sativa), 3'ss of exon 11
atgatatgggtgcctctgtccatctgtcagttgtatctctgcttgtcgctgttcggtgtggagtttctgttaacaatcatattgtac--ctttttcccgcagGAATTACAATTGCCGAGTATTTTCGTGATATGGGCTACAACGTTAGTATGATGGCTGACTCCACCTCACGATGGGCTGAGGCTTTGCGTGAGATCTCAGG
 |    | ||| | | ||  |  || |  ||  | | |   | |   | |  ||      ||  |  |  |||  |  || || ||   ||||  ||| |||||||||| || || |||||||  ||||| ||||| ||||| || || ||||||||||| ||||||||||||||||||||||| |||||||| || || ||
-ttgctttggt-catttggactgctatatgtattttatggaccttaagttcatcaccaatgatctcattgtaaacaaaatcttatatgactttgccccccagGAATTACGATAGCTGAGTATTACCGTGACATGGGTTACAATGTCAGCATGATGGCTGATTCCACCTCACGATGGGCTGAGGCATTGCGTGAAATTTCTGG

upper sequence: GRMZM2G128877_T03 (Zea mays), 3'ss of exon 8
lower sequence: AT1G78900.2 (Arabidopsis thaliana), 3'ss of exon 12
atgatat--gggtgcctctgtccatctgtcagttgtatctctgcttgtcgctgttcggtgtggagtttctgttaacaatcatattgtacctttttcccgcagGAATTACAATTGCCGAGTATTTTCGTGATATGGGCTACAACGTTAGTATGATGGCTGACTCCACCTCACGATGGGCTGAGGCTTTGCGTGAGATCTCAGG
 | || |   ||  |     |  |   || | |  |   ||   ||| |  || ||       | ||| | ||     |  || |||   ||       ||||||| ||||| || || |||||| | |||||||||||||| |||||||||||||| ||||| || || || ||||| || || ||  | || || |||||
gtaatgttcaggcacacagatttaatagttattgatgaatcccattgcctatgctc-------attttttttttttttttttaatgtgaattc------cagGAATCACAATCGCTGAATATTTTAGAGATATGGGCTACAATGTTAGTATGATGGCAGACTCAACTTCCCGTTGGGCAGAAGCATTAAGAGAAATTTCAGG

upper sequence: GRMZM2G128877_T03 (Zea mays), 3'ss of exon 8
lower sequence: Vv04s0008g02580.t01 (Vitis vinifera), 3'ss of exon 12
atgatatgggtgcctctgtccatctgtcagttgtatctctgcttgtcgc-tgttcggtgtggagtttctgttaacaatcatattgtacctttttcccgcagGAATTACAATTGCCGAGTATTTTCGTGATATGGGCTACAACGTTAGTATGATGGCTGACTCCACCTCACGATGGGCTGAGGCTTTGCGTGAGATCTCAGG
 |   || |||  || | |     ||  ||    || | | |  ||    | |      |  |  || | ||   || ||   ||  | |        |||| || ||||||||||| || ||| | || ||||| ||||| || ||||||||||| || || || || || ||||||||||||||||||||||| || ||
tttccattggtagcttttttttggtga-agcaacatttttccaagttttgtatatttattcaaaattattttctaaaccaatgtgatcatggaatgttcagGTATCACAATTGCCGAATACTTTAGAGACATGGGTTACAATGTCAGTATGATGGCAGATTCAACATCTCGTTGGGCTGAGGCTTTGCGTGAGATATCTGG

upper sequence: GRMZM2G128877_T03 (Zea mays), 3'ss of exon 8
lower sequence: Vv09s0054g00890.t01 (Vitis vinifera), 3'ss of exon 12
----atgatatgggtgcctctgtccatctgtcagttgtatctctgcttgtcgctgttcggtgtggagtttctgttaacaatcatattgtacctttttcccgcagGAATTACAATTGCCGAGTATTTTCGTGATATGGGCTACAACGTTAGTATGATGGCTGACTCCACCTCACGATGGGCTGAGGCTTTGCGTGAGATCTCAGG
    | | | |  |||    |||| |||       |||  |  || |       || | | |  ||  ||||   |  |||   |||||   ||||||    ||| || || || || || || ||  | |||||||||||||| |||||||||||||| || || || || |||||||| ||||| ||||| || || |||||
cctgaagcttttagtggtcttgtctatcacctttgtgttaccttgttatggaaggtgctgagatgatgttctccaactaatatgattgtgggtttttc----agGTATCACTATAGCTGAATACTTCAGAGATATGGGCTACAATGTTAGTATGATGGCAGATTCAACATCTCGATGGGCAGAGGCATTGCGAGAAATATCAGG

upper sequence: GRMZM2G128877_T03 (Zea mays), 3'ss of exon 8
lower sequence: EFJ33015 (Selaginella moellendorffii), 3'ss of exon 11
atgatatgggtgcctctgtccatctgtcagttgtatctctgcttgtcgctgttcggtgtggagtttctgttaacaatcatattgtacctttttcccgcagGAATTACAATTGCCGAGTATTTTCGTGATATGGGCTACAACGTTAGTATGATGGCTGACTCCACCTCACGATGGGCTGAGGCTTTGCGTGAGATCTCAGG
                                           | |  |  | |  |   |  |    | |    ||  ||| |    |||      |||| |||||  | || |||||||| ||||| |||||||| || || ||||||||||||||||| || ||  ||||||| || || |||||||| || || ||
------------------------------------------gtatgtccttccaattcaggctcagcgctg---attttatcgatggttt------cagGCATTACTCTGGCTGAGTATTTCCGTGACATGGGCTATAATGTCAGTATGATGGCTGACTCGACGTCGAGATGGGCCGAAGCCTTGCGTGAAATATCCGG

upper sequence: GRMZM2G128877_T03 (Zea mays), 3'ss of exon 8
lower sequence: EFJ30330 (Selaginella moellendorffii), 3'ss of exon 12
atgatatgggtgcctctgtccatctgtcagttgtatctctgcttgtcgctgttcggtgtggagtttctgttaacaatcatattgtacctttttcccgcagGAATTACAATTGCCGAGTATTTTCGTGATATGGGCTACAACGTTAGTATGATGGCTGACTCCACCTCACGATGGGCTGAGGCTTTGCGTGAGATCTCAGG
                                                 | |    |    | |     | |||  | || || |   |  || |   ||| |||||  | || |||||||| ||||| |||||||| || || ||||||||||||||||| || ||  ||||||| || || |||||||| || || ||
------------------------------------------------gtatgtccttccaattcaggctcaacgctgattttatcgatggtttc---agGCATTACTCTGGCTGAGTATTTCCGTGACATGGGCTATAATGTCAGTATGATGGCTGACTCGACGTCGAGATGGGCCGAAGCCTTGCGTGAAATATCCGG

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|31360171|gb|CD444528.1|CD444528
EST:     TAACACATCAAATATGCCTGTTGCTGCTCGTGAAGCCTCCATTTATACAG                         GAATTACAATTGCCGAGTATTTTCGTGATATGGGCTACAACGTTAGTATGA
genomic: TAACACATCAAATATGCCTGTTGCTGCTCGTGAAGCCTCCATTTATACAGgtaaaactct ... tttcccgcagGAATTACAATTGCCGAGTATTTTCGTGATATGGGCTACAACGTTAGTATGA






















 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tcgctgttcggtgtggagtttctgttaacaatcatattgtacctttttcccgcagGAATTACAATTGCCGAGTATTTTCGTGATATGGGCTACAACGTTAGTATGATGGCTGACTCCACCTCACGATGGGCTGAGGCTTTGCGTGAGATCTCAGG
                      tgttaac  putative branch site (score: 2)
                                    ttgtacctttttccc  putative PPT
                        ttaacaatcatatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
atgatatgggtgcctctgtccatctgtcagttgtatctctgcttgtcgctgttcggtgtggagtttctgttaacaatcatattgtacctttttcccgcagGAATTACAATTGCCGAGTATTTTCGTGATATGGGCTACAACGTTAGTATGATGGCTGACTCCACCTCACGATGGGCTGAGGCTTTGCGTGAGATCTCAGG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGATC
- - - - - -gcctctg
- - - - - - - - - -ccatctg
- - - - - - - - - - - - - - - - - - - -tgcttgt
- - - - - - - - - - - - - - - - - - - - - - - -gctgttc