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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagctctatcaggcatcctcgatcggatggctggagccaggcagatgctagccatctgccattcatcaggatacatatatatattatgttctctgtcaaattccgaatctttacagctgcgttgtatatatctccactgcccagGTTCCCTCCGATCACCTGCTCCGCGTACCTGTCCCAGCGCTACAAGGACACTCACGCGGATCTGAAATCCTACGACGACAGCAAGGCCTGATCAGAGGAC

Basic information

species Zea mays
transcript GRMZM2G147882_T04
intron # 10
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G147882_T01 (Zea mays), 3'ss of exon 9
lower sequence: LOC_Os01g09300.2 (Oryza sativa), 3'ss of exon 10
gtaagctctatcaggcatcctcgatcggatggctggagccagg-cagatgctagccatctgccattcatcaggatacatatatatattatgttctctgtcaaattccgaatctttacagctgcgttgtatatatc-tccactgcccagGTTCCCTCCGATCACCTGCTCCGCGTACCTGTCCCAGCGCTACAAGGACACTCACGCGGATCTGAAATCCTACGACGACAGCAAGGCCTGATCAGAGGAC
                                     |  ||| || || |           ||    ||||   |  |  |||     |||||    |||    |||   |   | |       ||| | |  | |   |   ||||||||||||||||||| ||||| || ||||| || ||||| |||||||| || || || |||||||   | |||  |  || ||||||||     |   | 
-------------------------------------gtaaggacacattccctttgatgatcacaattcagcccatgtccataaccattgttcatcttca----ccggggcg--agaaacataatgtgtgttccattgtccaaccagGTTCCCTCCGATCACTTGCTCGGCATACCTATCGCAGCGGTACAAGGATACGCATGCCGATCTGACCGCTTACAGCAGCAACAAGGCCTAGAAGGCCAAG

upper sequence: GRMZM2G147882_T01 (Zea mays), 3'ss of exon 9
lower sequence: Vv11s0016g03200.t01 (Vitis vinifera), 3'ss of exon 10
gtaagctctatcaggcatcctcgatcggatggctggagccaggcagatgctagccatctgccattcatcaggatacatatatatattatgttctctgtcaaattccgaatctttacagctgcgttgtat-atatctccactgc-ccagGTTCCCTCCGATCACCTGCTCCGCGTACCTGTCCCAGCGCTACAAGGACACTCACGCGGATCTGAAATCCTACGACGACAGCAAGGCCTGATCAGAGGAC
                                         ||||| ||| |   |     |||  |     |   ||  | |  |||| |    |||  | ||     ||||   | |    ||| || ||| ||  | |   |||| || |||||  |||  ||     | |||||| |||||||||||||||| ||||| || |||||||| |  |||    |     | || |||  | |    
--------------------------------------ggtggcagttgcaaaata-----cataaactgcaaggtattaagacgttatatctgttgtacactt-----tcttgttaaccatattgaattatacctttattctgccagATTTCCTCCAGTCAAATGTGGGACTTACCTGACCCAGCGCTACAAGGATACTCATGCTGATCTGAATTTGTACACTAAACATCAAGCTTGAAAAAATTTG
















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|78077655|gb|DV506089.1|DV506089
EST:     TGCGTGGTGGAGTGCCTGCCGACCTGCAAGTCCGAATCAAATCCTCCAAA                         GTTCCCTCCGATCACCTGCTCCGCGTACCTGTCCCAGCGCTACAAGGACAC
genomic: TGCGTGGTGGAGTGCCTGCCGACCTGCAAGTCCGAATCAAATCCTCCAAAgtaagctcta ... cactgcccagGTTCCCTCCGATCACCTGCTCCGCGTACCTGTCCCAGCGCTACAAGGACAC
EST: gi|32926415|gb|CF031227.1|CF031227
EST:     TGCGTGGTGGAGTGCCTGCCGACCTGCAAGTCCGAATCAAATCCTCCAAA                         GTTCCCTCCGATCACCTGCTCCGCGTACCT
genomic: TGCGTGGTGGAGTGCCTGCCGACCTGCAAGTCCGAATCAAATCCTCCAAAgtaagctcta ... cactgcccagGTTCCCTCCGATCACCTGCTCCGCGTACCT
EST: gi|32926466|gb|CF031278.1|CF031278
EST:     TGCGTGGTGGAGTGCCTGCCGACCTGCAAGTCCGAATCAAATCCTCCAAA                         GTTCCCTCCGATCACCTGCTCCGCGCACCT
genomic: TGCGTGGTGGAGTGCCTGCCGACCTGCAAGTCCGAATCAAATCCTCCAAAgtaagctcta ... cactgcccagGTTCCCTCCGATCACCTGCTCCGCGTACCT
EST: gi|74241069|gb|DT648983.1|DT648983
EST:     TGCGTGGTGGAGTGCCTGCCGACCTGCAAGTCCGAATCAAATCCTCCAAA                         GTTCCCTCCGATCACCTGCTCCGCGTACCTGTCCCAGCGCTACAAGGACAC
genomic: TGCGTGGTGGAGTGCCTGCCGACCTGCAAGTCCGAATCAAATCCTCCAAAgtaagctcta ... cactgcccagGTTCCCTCCGATCACCTGCTCCGCGTACCTGTCCCAGCGCTACAAGGACAC
EST: gi|32926635|gb|CF031447.1|CF031447
EST:     TGCGTGGTGGAGTGCCTGCCGACCTGCAAGTCCGAATCAAATCCTCCAAA                         GTTCCCTCCGATCACCTGCTCCGCGT
genomic: TGCGTGGTGGAGTGCCTGCCGACCTGCAAGTCCGAATCAAATCCTCCAAAgtaagctcta ... cactgcccagGTTCCCTCCGATCACCTGCTCCGCGT
EST: gi|32926849|gb|CF031661.1|CF031661
EST:     TGCGTGGTGGAGTGCCTGCCGACCTGCAAGTCCGAATCAAATCCTCCAAA                         GTTCCCTCCGATCACCTGCTCCGCGT
genomic: TGCGTGGTGGAGTGCCTGCCGACCTGCAAGTCCGAATCAAATCCTCCAAAgtaagctcta ... cactgcccagGTTCCCTCCGATCACCTGCTCCGCGT
EST: gi|32926430|gb|CF031242.1|CF031242
EST:     TGCGTGGTGGAGTGCCTGCCGACCTGCAAGTCCGAATCAAATCCTCCAAA                         GTTCCCTCCGATCACCTGCTCCGCGTACCT
genomic: TGCGTGGTGGAGTGCCTGCCGACCTGCAAGTCCGAATCAAATCCTCCAAAgtaagctcta ... cactgcccagGTTCCCTCCGATCACCTGCTCCGCGTACCT
EST: gi|32926417|gb|CF031229.1|CF031229
EST:     TGCGTGGTGGAGTGCCTGCCGACCTGCAAGTCCGAATCAAATCCTCCAAA                         GTTCCCTCCGATCACCTGCTCCGCGTACCT
genomic: TGCGTGGTGGAGTGCCTGCCGACCTGCAAGTCCGAATCAAATCCTCCAAAgtaagctcta ... cactgcccagGTTCCCTCCGATCACCTGCTCCGCGTACCT
EST: gi|32925395|gb|CF030207.1|CF030207
EST:     TGCGTGGTGGAGTGCCTGCCGACCTGCAAGTCCGAATCAAATCCTCCAAA                         GTTCCCTCCGATCACCTGCTCCGCGT
genomic: TGCGTGGTGGAGTGCCTGCCGACCTGCAAGTCCGAATCAAATCCTCCAAAgtaagctcta ... cactgcccagGTTCCCTCCGATCACCTGCTCCGCGT
EST: gi|211415426|gb|FL477512.1|FL477512
EST:     TGCGTGGTGGAGTGCCTGCCGACCTGCAAGTCCGAATCAAATCCTCCAAA                         GTTCCCTCCGATCACCTGCTCCGCGTACCTGTCCCAGCGCTACAAGGACAC
genomic: TGCGTGGTGGAGTGCCTGCCGACCTGCAAGTCCGAATCAAATCCTCCAAAgtaagctcta ... cactgcccagGTTCCCTCCGATCACCTGCTCCGCGTACCTGTCCCAGCGCTACAAGGACAC
EST: gi|211525267|gb|FL432922.1|FL432922
EST:     TGCGTGGTGGAGTGCCTGCCGACCTGCAAGTCCGAATCAAATCCTCCAAA                         GTTCCCTCCGATCACCTGCTCCGCGTACCTGTCCCAGCGCTACAAGGACAC
genomic: TGCGTGGTGGAGTGCCTGCCGACCTGCAAGTCCGAATCAAATCCTCCAAAgtaagctcta ... cactgcccagGTTCCCTCCGATCACCTGCTCCGCGTACCTGTCCCAGCGCTACAAGGACAC
EST: gi|71758494|gb|DR956431.1|DR956431
EST:     TGCGTGGTGGAGTGCCTGCCGACCTGCAAGTCCGAATCAAATCCTCCAAA                         GTTCCCTCCGATCACCTGCTCCGCGTACCTGTCCCAGCGCTACAAGGACAC
genomic: TGCGTGGTGGAGTGCCTGCCGACCTGCAAGTCCGAATCAAATCCTCCAAAgtaagctcta ... cactgcccagGTTCCCTCCGATCACCTGCTCCGCGTACCTGTCCCAGCGCTACAAGGACAC
EST: gi|32926166|gb|CF030978.1|CF030978
EST:     TGCGTGGTGGAGTGCCTGCCGACCTGCAAGTCCGAATCAAATCCTCCCAA                         GTTCCCTCCGATCACCTGCTCCGCGTACCT
genomic: TGCGTGGTGGAGTGCCTGCCGACCTGCAAGTCCGAATCAAATCCTCCAAAgtaagctcta ... cactgcccagGTTCCCTCCGATCACCTGCTCCGCGTACCT
EST: gi|32926025|gb|CF030837.1|CF030837
EST:     TGCGTGGTGGAGTGCCTGCCGACCTGCAAGTCCGAATCAAATCCTCCAAA                         GTTCCCTCCGATCACCTGCTCCGCGTACCT
genomic: TGCGTGGTGGAGTGCCTGCCGACCTGCAAGTCCGAATCAAATCCTCCAAAgtaagctcta ... cactgcccagGTTCCCTCCGATCACCTGCTCCGCGTACCT
EST: gi|71299018|gb|DR785501.1|DR785501
EST:     TGCGTGGTGGAGTGCCTGCCGACCTGCAAGTCCGAATCAAATCCTCCAAA                         GTTCCCTCCGATCACCTGTTCCGCGTACCTGTCCCAGCGCTACAAGGACAC
genomic: TGCGTGGTGGAGTGCCTGCCGACCTGCAAGTCCGAATCAAATCCTCCAAAgtaagctcta ... cactgcccagGTTCCCTCCGATCACCTGCTCCGCGTACCTGTCCCAGCGCTACAAGGACAC
EST: gi|32925152|gb|CF029964.1|CF029964
EST:     TGCGTGGTGGAGTGCCCGCCGACCTGCAAGTCCGAATCAAATCCTCCAAA                         GTTCCCTCCGATCACCTGCTCCGCGT
genomic: TGCGTGGTGGAGTGCCTGCCGACCTGCAAGTCCGAATCAAATCCTCCAAAgtaagctcta ... cactgcccagGTTCCCTCCGATCACCTGCTCCGCGT
EST: gi|71429425|gb|DR810475.1|DR810475
EST:     TGCGTGGTGGAGTGCCTGCCGACCTGCAAGTCCGAATCAAATCCTCCAAA                         GTTCCCTCCGATCACCTGCTCCGCGTACCTGTCCCAGCGCTACAAGGACAC
genomic: TGCGTGGTGGAGTGCCTGCCGACCTGCAAGTCCGAATCAAATCCTCCAAAgtaagctcta ... cactgcccagGTTCCCTCCGATCACCTGCTCCGCGTACCTGTCCCAGCGCTACAAGGACAC
EST: gi|76287314|gb|DV026882.1|DV026882
EST:     TGCGTGGTGGAGTGCCTGCCGACCTGCAAGTCCGAATCAAATCCTCCAAA                         GTTCCCTCCGATCACCTGCTCCGCGTACCTGTCCCAGCGCTACAAGGACAC
genomic: TGCGTGGTGGAGTGCCTGCCGACCTGCAAGTCCGAATCAAATCCTCCAAAgtaagctcta ... cactgcccagGTTCCCTCCGATCACCTGCTCCGCGTACCTGTCCCAGCGCTACAAGGACAC
EST: gi|32926219|gb|CF031031.1|CF031031
EST:     TGCGTGGTGGAGTGCCTGCCGACCTGCAAGTCCGAATCAAATCCTCCAAA                         GTTCCCTCCGATCACCTGCTCCGCGTACCT
genomic: TGCGTGGTGGAGTGCCTGCCGACCTGCAAGTCCGAATCAAATCCTCCAAAgtaagctcta ... cactgcccagGTTCCCTCCGATCACCTGCTCCGCGTACCT
EST: gi|78021585|gb|DV489972.1|DV489972
EST:     TGCGTGGTGGAGTGCCTGCCGACCTGCAAGTCCGAATCAAATCCTCCAAA                         GTTCCCTCCGATCACCTGCTCCGCGTACCTGTCCCAGCGCTACAAGGACAC
genomic: TGCGTGGTGGAGTGCCTGCCGACCTGCAAGTCCGAATCAAATCCTCCAAAgtaagctcta ... cactgcccagGTTCCCTCCGATCACCTGCTCCGCGTACCTGTCCCAGCGCTACAAGGACAC
EST: gi|78078283|gb|DV506698.1|DV506698
EST:     TGCGTGGTGGAGTGCCTGCCGACCTGCAAGTCCGAATCAAATCCTCCAAA                         GTTCCCTCCGATCACCTGCTCCGCGTACCTGTCCCAGCGCTACAAGGACAC
genomic: TGCGTGGTGGAGTGCCTGCCGACCTGCAAGTCCGAATCAAATCCTCCAAAgtaagctcta ... cactgcccagGTTCCCTCCGATCACCTGCTCCGCGTACCTGTCCCAGCGCTACAAGGACAC
EST: gi|32858735|gb|CD998416.1|CD998416
EST:     TGCGTGGTGGAGTGCCTGCCGACCTGCAAGTCCGAATCAAATCCTCCAAA                         GTTCCCTCCGATCACCTGCTCCGCGTACCTGTCCCAGCGCTACAAGGACAC
genomic: TGCGTGGTGGAGTGCCTGCCGACCTGCAAGTCCGAATCAAATCCTCCAAAgtaagctcta ... cactgcccagGTTCCCTCCGATCACCTGCTCCGCGTACCTGTCCCAGCGCTACAAGGACAC
EST: gi|32926072|gb|CF030884.1|CF030884
EST:     TGCGTGGTGGAGTGCCTGCCGACCTGCAAGTCCGAATCAAATCCTCCAAA                         GTTCCCTCCGATCACCTGCTCCGCGTACCT
genomic: TGCGTGGTGGAGTGCCTGCCGACCTGCAAGTCCGAATCAAATCCTCCAAAgtaagctcta ... cactgcccagGTTCCCTCCGATCACCTGCTCCGCGTACCT
EST: gi|32926162|gb|CF030974.1|CF030974
EST:     TGCGTGGTGGAGTGCCTGCCGACCTGCAAGTCCGAATCAAATCCTCCAAA                         GTTCCCTCCGATCACCTGCTCCGCGTACCT
genomic: TGCGTGGTGGAGTGCCTGCCGACCTGCAAGTCCGAATCAAATCCTCCAAAgtaagctcta ... cactgcccagGTTCCCTCCGATCACCTGCTCCGCGTACCT
EST: gi|32926197|gb|CF031009.1|CF031009
EST:     TGCGTGGTGGAGTGCCTGCCGACCTGCAAGTCCGAATCAAATCCTCCAAA                         GTTCCCTCCGATCACCTGCTCCGCGTACCT
genomic: TGCGTGGTGGAGTGCCTGCCGACCTGCAAGTCCGAATCAAATCCTCCAAAgtaagctcta ... cactgcccagGTTCCCTCCGATCACCTGCTCCGCGTACCT
EST: gi|32925587|gb|CF030399.1|CF030399
EST:     TGCGTGGTGGAGTGCCTGCCGACCTGCAAGTCCGAATCAAATCCTCCAAA                         GTTCCCTCCGATCACCTGCTCCGCGT
genomic: TGCGTGGTGGAGTGCCTGCCGACCTGCAAGTCCGAATCAAATCCTCCAAAgtaagctcta ... cactgcccagGTTCCCTCCGATCACCTGCTCCGCGT
EST: gi|32925272|gb|CF030084.1|CF030084
EST:     TGCGTGGTGGAGTGCCTGCCGACCTGCAAGTCCGAATCAAATCCTCCAAA                         GTTCCCTCCGATCACCTGCTCCGCGT
genomic: TGCGTGGTGGAGTGCCTGCCGACCTGCAAGTCCGAATCAAATCCTCCAAAgtaagctcta ... cactgcccagGTTCCCTCCGATCACCTGCTCCGCGT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tctctgtcaaattccgaatctttacagctgcgttgtatatatctccactgcccagGTTCCCTCCGATCACCTGCTCCGCGTACCTGTCCCAGCGCTACAAGGACACTCACGCGGATCTGAAATCCTACGACGACAGCAAGGCCTGATCAGAGGAC
                                         tctccact  CT-rich tract
                                ttgtatatat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaagctctatcaggcatcctcgatcggatggctggagccaggcagatgctagccatctgccattcatcaggatacatatatatattatgttctctgtcaaattccgaatctttacagctgcgttgtatatatctccactgcccagGTTCCCTCCGATCACCTGCTCCGCGTACCTGTCCCAGCGCTACAAGGACACTCACGCGGATCTGAAATCCTACGACGACAGCAAGGCCTGATCAGAGGAC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAGGA