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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...aaaagggagacgaaaatacatgtttttctggcacgtgttcttgtttaatttttgttaccagtatcgttgtttgccattttttaattgtttgtttctgcagCCGTGCCTGTCGAAAATGGCAAATTCCTTCTATCCGCAAAAAGGAACTGCCGTGCAACATATACAGAATATATAATATCAATAAATTCTGGTGATACATC

Basic information

species Zea mays
transcript GRMZM2G046816_T04
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G046816_T04 (Zea mays), 3'ss of exon 3
lower sequence: LOC_Os11g06420.2 (Oryza sativa), 3'ss of exon 3
aaaagggagacgaaaatacatgtttttctggcacgtgttcttgtttaatttttgttaccagtatc--gttgtttgccattttttaattgtttgtttctgcagCCGTGCCTGTCGAAAATGGCAAATTCCTTCTATCCGCAAAAAGGAACTGCCGTGCAACATATACAGAATATATAATATCAATAAATTCTGGTGATACATC
 |  ||   ||  | ||   |  ||| || ||  |  | ||| |   ||||  || ||||| ||    |  |||   || |||| |||     |||||||||| |||| ||| || |||||||||||||||||||| |||||||| ||||| | |||||||| |||||||||| | ||||| || ||| ||    ||  |||
-actggtgcacatatatgttttgtttccttgctggaatacttttagtatttcagt-accagcatttactaattttagatgttttgatttcccttttctgcagCTGTGCTTGTTGACAATGGCAAATTCCTTCTATCAGCAAAAAGAAACTGGCATGCAACATGTACAGAATATGTGATATCTATGAATGCTAACAATTTATC
















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|31355846|gb|CD440203.1|CD440203
EST:     GAGGGATAAATCTACCCAACTCTACAGTCTGTACCTTAGTTTTAGCTCTG                         CCGTGCCTGTCGAAAATGGCAAATTCCTTCTATCCGCAAAAAGGAACTGCC
genomic: GAGGGATACATCTACCCAAATCTACAGTCTGTACCTTAGTTTTAGCTCTGgtaagtctat ... gtttctgcagCCGTGCCTGTCGAAAATGGCAAATTCCTTCTATCCGCAAAAAGGAACTGCC
EST: gi|31360425|gb|CD444782.1|CD444782
EST:     GAGGGATAAATCTACCCAAATCTACAGTCTGTACCTTAGTTTTAGCTCTG                         CCGTGCCTGTCGAAAATGGCAAATTCCTTCTATCCGCAAAAAGGAACTGCC
genomic: GAGGGATACATCTACCCAAATCTACAGTCTGTACCTTAGTTTTAGCTCTGgtaagtctat ... gtttctgcagCCGTGCCTGTCGAAAATGGCAAATTCCTTCTATCCGCAAAAAGGAACTGCC
EST: gi|67042292|gb|CO468547.1|CO468547
EST:     GAGGGATATTTCTCCCCAAATCTACAGTCTGTACCTTAGTTTTAGCTCTG                         CCGTGCCTGTCGAAAATGGCAAATTCCTTCTATCCGCAAAAAGGAACTGCC
genomic: GAGGGATACATCTACCCAAATCTACAGTCTGTACCTTAGTTTTAGCTCTGgtaagtctat ... gtttctgcagCCGTGCCTGTCGAAAATGGCAAATTCCTTCTATCCGCAAAAAGGAACTGCC
EST: gi|22819363|gb|BU499453.1|BU499453
EST:     GAGGGATACATCTACCCAAATCTACAGTCTGTACCTTAGTTTTAGCTCTG                         CCGTGCCTGTCGAAAATGGCAAATTCCTTCTATCCGCAAAAAGGAACTGCC
genomic: GAGGGATACATCTACCCAAATCTACAGTCTGTACCTTAGTTTTAGCTCTGgtaagtctat ... gtttctgcagCCGTGCCTGTCGAAAATGGCAAATTCCTTCTATCCGCAAAAAGGAACTGCC
EST: gi|26559903|gb|CA832138.1|CA832138
EST:     GAGGGATACATCTACCCAAATCTACAGTCTGTACCTTAGTTTTAGCTCTG                         CCGTGCCTGTCGAAAATGGCAAATTCCTTCTATCCGCAAAAAGGAACTGCC
genomic: GAGGGATACATCTACCCAAATCTACAGTCTGTACCTTAGTTTTAGCTCTGgtaagtctat ... gtttctgcagCCGTGCCTGTCGAAAATGGCAAATTCCTTCTATCCGCAAAAAGGAACTGCC
EST: gi|87156288|gb|DY401077.1|DY401077
EST:     GAGGGATACATCTACCCAAATCTACAGTCTGTACCTTAGTTTTAGCTCTG                         CCGTGCCTGTCGAAAATGGCAAATTCCTTCTATCCGCAAAAAGGAACTGCC
genomic: GAGGGATACATCTACCCAAATCTACAGTCTGTACCTTAGTTTTAGCTCTGgtaagtctat ... gtttctgcagCCGTGCCTGTCGAAAATGGCAAATTCCTTCTATCCGCAAAAAGGAACTGCC
EST: gi|74238493|gb|DT646407.1|DT646407
EST:     GAGGGATACATCTACCCAAATCTACAGTCTGTACCTTAGTTTTAGCTCTG                         CCGTGCCTGTCGAAAATGGCAAATTCCTTCTATCCGCAAAAGGGA-CTGCC
genomic: GAGGGATACATCTACCCAAATCTACAGTCTGTACCTTAGTTTTAGCTCTGgtaagtctat ... gtttctgcagCCGTGCCTGTCGAAAATGGCAAATTCCTTCTATCCGCAAAAAGGAACTGCC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

taatttttgttaccagtatcgttgtttgccattttttaattgtttgtttctgcagCCGTGCCTGTCGAAAATGGCAAATTCCTTCTATCCGCAAAAAGGAACTGCCGTGCAACATATACAGAATATATAATATCAATAAATTCTGGTGATACATC
                                 ttttaat  putative branch site (score: 3)
                                          tttgtttct  putative PPT
                              attttttaattgtttg  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
aaaagggagacgaaaatacatgtttttctggcacgtgttcttgtttaatttttgttaccagtatcgttgtttgccattttttaattgtttgtttctgcagCCGTGCCTGTCGAAAATGGCAAATTCCTTCTATCCGCAAAAAGGAACTGCCGTGCAACATATACAGAATATATAATATCAATAAATTCTGGTGATACATC

- - - - - - - -atacatg
- - - - - - - - - - - - -ttctggc
- - - - - - - - - - - - - - - - - - gttcttg
- - - - - - - - - - - - - - - - - - - - - - - - -ttttgtt
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ttgtttg