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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgagaacattgccatggtatttttttttgtagttccctcgtagttgcacagctttacttactgagataaggtcaacactggacatggcctggacctatgatctctaaggtcacagtttctcgcctttggtaaaacttgctcttatgtaacgacagcaagaaaactgatctaagacctgcattttggtgaattttgcagCTGTACAAGACAGGGATCACAAATTCTTGACAAAAGCAGTGGAAGAAGCATACCGAGGAGTCGATTGCGGCGATGGAGGTCCATTTGGAGCAGTTGTCGT

Basic information

species Zea mays
transcript GRMZM2G082924_T01
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G082924_T01 (Zea mays), 3'ss of exon 2
lower sequence: LOC_Os07g14150.5 (Oryza sativa), 3'ss of exon 1
gtgagaacattgccatggtatttttttttgtagttccctcgtagttgcacagctttacttactgagataaggtcaacactggacatggcctggacctatgatctctaaggtcacagtttctcgcctttggtaaaacttgctcttatgtaacgacagcaagaaaactgatctaa----gacctgcattttggtgaattttgcagCTGTACAAGACAGGGATCACAAATTCTTGACAAAAGCAGTGGAAGAAGCATACCGAGGAGTCGATTGCGGCGATGGAGGTCCATTTGGAGCAGTTGTCGT
                                                           ||     | ||        ||| |   | | |     | ||||||  |    | ||| ||      |||||   |  | |  |   | ||| | |  | |||| |      ||      || ||  ||||||  || ||| ||||||| ||||| || || ||||||||||||||||||||||| |||||||| ||||| ||||| || ||||| |||||||| || ||||||||||| || ||
----------------------------------------------------------gtaagagtaaaataatgcttctgcattagtcttctcagtttgatctgcag---cccagctttcactgtttgggtgatttggggcgcttttaaggtcttccagaagaactgcttagtgttaacttgagttttggaaaaatttacagCTGTGCAAGATAGAGACCACAAATTCTTGACAAAAGCAGTTGAAGAAGCGTACCGGGGAGTTGACTGCGGTGATGGAGGCCCCTTTGGAGCAGTCGTTGT

upper sequence: GRMZM2G082924_T01 (Zea mays), 3'ss of exon 2
lower sequence: GLYMA20G37210.1 (Glycine max), 3'ss of exon 2
gtgagaacattgccatggtatttttttttgtagttccctcgtagttgcacagctttacttactgagataaggtcaacactggacatggcctggacctatgatctctaaggtcacagtttctcgcctttggtaaaacttgctcttatgtaacgacagcaagaaaactgatctaagacctgcattttggtgaattttgcagCTGTACAAGACAGGGATCACAAATTCTTGACAAAAGCAGTGGAAGAAGCATACCGAGGAGTCGATTGCGGCGATGGAGGTCCATTTGGAGCAGTTGTCGT
                                                                                                         || | | | | ||  ||   | || |         || | || |||     |    | | |  | | | || |   |||   |   | |  |||||||||| || || || ||||| ||||| ||||||||||| ||||||||||||   || || || || || |||||||| ||||||||||||||||| ||
--------------------------------------------------------------------------------------------------------gtatgataataattgatcatttctgtt---------tcatctgcaacccaccctcccacatttttttcaaacgttattttctcttgttataccagCTGTACAGGATAGAGACCACAAGTTCTTAACAAAAGCAGTTGAAGAAGCATACAAGGGGGTTGAATGTGGTGATGGAGGCCCATTTGGAGCAGTTGTTGT
















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|30160666|gb|CB924395.1|CB924395
EST:     AAAGGATGGAACCATCTCAGTTGCTTCTGCATTTGCTGCTCATCAGGAAG                         CTGTGCAAGACAGGGATCACAAATTCTTGACAAAAGCAGTGGAAGAAGCAT
genomic: AAAGGATGGAACCATCTCAGTTGCTTCTGCATTTGTTGCTCATCAGGAAGgtgagaacat ... aattttgcagCTGTACAAGACAGGGATCACAAATTCTTGACAAAAGCAGTGGAAGAAGCAT
EST: gi|31628205|gb|CD526493.1|CD526493
EST:     AAAGGATGGAACCATCTCAGTTGCTTCTGCATTTGCTGCTCATCAGGAAG                         CTGTGCAAGACAGGGATCACAAATTCTTGACAAAAGCAGTGGAAGAAGCAT
genomic: AAAGGATGGAACCATCTCAGTTGCTTCTGCATTTGTTGCTCATCAGGAAGgtgagaacat ... aattttgcagCTGTACAAGACAGGGATCACAAATTCTTGACAAAAGCAGTGGAAGAAGCAT
EST: gi|24462578|gb|BM660109.1|BM660109
EST:     AAAGGATGGAACCATCTCAGTTGCTTCTGCATTTGCTGCTCATCAGGAAG                         CTGTGCAAGACAGGGATCACAAATTCTTGACAAAAGCAGTGGAAGAAGCAT
genomic: AAAGGATGGAACCATCTCAGTTGCTTCTGCATTTGTTGCTCATCAGGAAGgtgagaacat ... aattttgcagCTGTACAAGACAGGGATCACAAATTCTTGACAAAAGCAGTGGAAGAAGCAT
EST: gi|15632335|gb|BI679428.1|BI679428
EST:     AAAGGATGGAACCATCTCAGTTGCTTCTGCATTTGCTGCTCATCAGGAAG                         CTGTGCAAGACAGGGATCACAAATTCTTGACAAAAGCAGTGGAAGAAGCAT
genomic: AAAGGATGGAACCATCTCAGTTGCTTCTGCATTTGTTGCTCATCAGGAAGgtgagaacat ... aattttgcagCTGTACAAGACAGGGATCACAAATTCTTGACAAAAGCAGTGGAAGAAGCAT
EST: gi|44681911|gb|CK786959.1|CK786959
EST:     AAAGGATGGAACCATCTCAGTTGCTTCTGCATTTGCTGCTCATCAGGAAG                         CTGTGCAAGACAGGGATCACAAATTCTTGACAAAAGCAGTGGAGGAAGCAT
genomic: AAAGGATGGAACCATCTCAGTTGCTTCTGCATTTGTTGCTCATCAGGAAGgtgagaacat ... aattttgcagCTGTACAAGACAGGGATCACAAATTCTTGACAAAAGCAGTGGAAGAAGCAT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atgtaacgacagcaagaaaactgatctaagacctgcattttggtgaattttgcagCTGTACAAGACAGGGATCACAAATTCTTGACAAAAGCAGTGGAAGAAGCATACCGAGGAGTCGATTGCGGCGATGGAGGTCCATTTGGAGCAGTTGTCGT
                  aactgat  putative branch site (score: 3)
                                           tgaatttt  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
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---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgagaacattgccatggtatttttttttgtagttccctcgtagttgcacagctttacttactgagataaggtcaacactggacatggcctggacctatgatctctaaggtcacagtttctcgcctttggtaaaacttgctcttatgtaacgacagcaagaaaactgatctaagacctgcattttggtgaattttgcagCTGTACAAGACAGGGATCACAAATTCTTGACAAAAGCAGTGGAAGAAGCATACCGAGGAGTCGATTGCGGCGATGGAGGTCCATTTGGAGCAGTTGTCGT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGCAG