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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtacttttttctgatcattttatactgaactgtttttttattaaaatttaagtttaatggttcttaaacctttcaaagttggtgtgatacaatcagaaatccaataatgaatgctacttagcatgtatgagctttatgaattgatttatcctatgaagtggactcatttattttgtggtcatgaagGAGCTGCTGGCTATTCAGCAGCAAGGACCTCGTGCAATAGGTTTCTTTGGAACCCGCAACATGGGATTTATGCACCAACAGCTTATTGAGATCCTGAGCT

Basic information

species Zea mays
transcript GRMZM2G081653_T02
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G081653_T02 (Zea mays), 3'ss of exon 2
lower sequence: LOC_Os01g23680.1 (Oryza sativa), 3'ss of exon 2
gtacttttttctgatcattttatactgaactgtttt--tttattaaa----atttaagtttaatggttctt--aaacct-ttcaaagttggtg--------tgatacaatcagaaatccaataatgaatgctacttagcatgtatgagctttatgaattgatttatcctatgaagtggactcatttattttgtggtcatgaagGAGCTGCTGGCTATTCAGCAGCAAGGACCTCGTGCAATAGGTTTCTTTGGAACCCGCAACATGGGATTTATGCACCAACAGCTTATTGAGATCCTGAGCT
||   ||| |||   | |||| || ||      ||   ||||  |||     |||  |  || | |||  |  |||  | ||    |                || |  |      ||    |||||||| ||  ||||||     |  | |||||| | ||||||  |||  | ||  || ||| | || ||||| ||| ||||| |||||||||||||||| || ||||| || || |||||||| ||||| ||||| |||||||| |||||||| |||||||||||||||||||||||||
gtggctttctctttcctttttctattgtgtccattcaatttaacaaagtcagtttttgcctagtagtttctgtaaatatgtttggggccaacagatatcttccatgctgttcatcctcatccaatgaatgataaatagcata----acatgtatgaaattatttatattatagaatgatcttattcacttagtggtaatgcagGAGTTGCTGGCTATTCAGCAACAGGGACCGCGGGCTATAGGTTTTTTTGGTACCCGTAACATGGGGTTTATGCATCAACAGCTTATTGAGATCCTGAGCT

upper sequence: GRMZM2G081653_T02 (Zea mays), 3'ss of exon 2
lower sequence: GLYMA07G40350.2 (Glycine max), 3'ss of exon 2
gtacttttttctgatcattttatactgaactgtttttttattaaaatttaagtttaatggttcttaaacctttcaaagttggtgtgatacaatcagaaatccaataatgaatgctacttagcatgtatgagctttatgaattgatttatcctatgaagtggactcatttattttgtggtcatgaagGAGCTGCTGGCTATTCAGCAGCAAGGACCTCGTGCAATAGGTTTCTTTGGAACCCGCAACATGGGATTTATGCACCAACAGCTTATTGAGATCCTGAGCT
                                                                            | ||| ||   |    |   | |  |  |      | ||   |||    | | |     |   || |  || | |       || |||   | ||| |||     |  ||||| |  |||| ||||| |||||||||||| | || || || || |||||||| || ||||||||||| ||||||||| | || |||||||| || ||||
----------------------------------------------------------------------------aattgttgccttgtgct---atactctttgtcctgtactg--tagtgcatgtcaaacacacccatag--ttgtacagcattttgaact---tcattatgtttctttacagGAGTTATTGGCCATTCAACAGCAAGGACCTAGAGCTATTGGCTTTTTTGGAACTCGGAACATGGGATTCATGCACCAAGAACTAATTGAGATTCTTAGCT

upper sequence: GRMZM2G081653_T02 (Zea mays), 3'ss of exon 2
lower sequence: GLYMA17G00330.1 (Glycine max), 3'ss of exon 2
gtacttttttctgatcattttatactgaactgtttttttattaaaatttaagtttaatggttcttaaacctttcaaagttggtgtgatacaatcagaaatccaataatgaatgctacttagcatgtatgagctttatgaattgatttatcctatgaagtggactcatttattttgtggtcatgaagGAGCTGCTGGCTATTCAGCAGCAAGGACCTCGTGCAATAGGTTTCTTTGGAACCCGCAACATGGGATTTATGCACCAACAGCTTATTGAGATCCTGAGCT
                                                                      ||| ||     || |       || |   |||  || ||  |   |   | ||   ||  ||    | | |||    |   | ||||  | | |   || |||| |        ||||| |  |||| ||||| |||||||||||| | || || || || |||||||| || ||||||||||| ||||||||| | || |||||||| || ||||
---------------------------------------------------------------------gttttaactcaagtat----ttgtccggt-tccggtagtgtgtatca---atcacacattcgcacccttagttgtacaacattttgaacagaatt---ttgttttttac------agGAGTTATTGGCCATTCAACAGCAAGGACCTAGAGCTATTGGCTTTTTTGGAACTCGGAACATGGGATTCATGCACCAAGAACTAATTGAGATTCTTAGCT

upper sequence: GRMZM2G081653_T02 (Zea mays), 3'ss of exon 2
lower sequence: EFJ38716 (Selaginella moellendorffii), 3'ss of exon 1
gtacttttttctgatcattttatactgaactgtttttttattaaaatttaagtttaatggttcttaaacctttcaaagttggtgtgatacaatcagaaatccaataatgaatgctacttagcatgtatgagctttatgaattgatttatcctatgaagtggactcatttattttgtggtcatgaagGAGCTGCTGGCTATTCAGCAGCAAGGACCTCGTGCAATAGGTTTCTTTGGAACCCGCAACATGGGATTTATGCACCAACAGCTTATTGAGATCCTGAGCT
                                                                                                      | |  | | | || ||    |    ||  | || |   ||| |||    |  | |||       ||| | |  |  |     |||| || || || || || || ||||| ||  | || || || ||||| ||||| || ||||||||||| ||||| ||||||||||||||||| || || |
---------------------------------------------------------------------------------------------------gtaagttcttagttct-ctcgaaactcttgttccttcttctttgtttt----tcgggagttcttatgtttttctcttcctttctcagGAACTTCTCGCGATCCAACAACAAGGGCCAAGAGCTATCGGCTTCTTCGGAACGCGAAACATGGGATTCATGCATCAACAGCTTATTGAGATACTTAGTT

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|50329846|gb|CO524972.1|CO524972
EST:     CGGTTGCTGAACCAGAATACAAGCAGATCCCAGATGTAGATTACCTACAG                         GAGCTGCTGGCTATTCAGCAGCAAGGACCTCGTGCAATAGGTTTCTTTGGA
genomic: CGGTTGCTGAACCAGAATACAAGCAGATCCCAGATGTAGATTACCTACAGgtactttttt ... ggtcatgaagGAGCTGCTGGCTATTCAGCAGCAAGGACCTCGTGCAATAGGTTTCTTTGGA
EST: gi|89764107|gb|DY691035.1|DY691035
EST:     GCAGATCCCAGATGTAGATTACCTACAG                         GAGCTGCTGGCTATTCAGCAGCAAGGACCTCGTGCAATAGGTTTCTTTGGA
genomic: GCAGATCCCAGATGTAGATTACCTACAGgtactttttt ... ggtcatgaagGAGCTGCTGGCTATTCAGCAGCAAGGACCTCGTGCAATAGGTTTCTTTGGA
EST: gi|78075488|gb|DV503922.1|DV503922
EST:     CGGTTGCTGAACCAGAATACAAGCAGATCCCAGATGTAGATTACCTACAG                         GAGCTGCTGGCTATTCAGCAGCAAGGACCTCGTGCAATAGGTTTCTTTGGA
genomic: CGGTTGCTGAACCAGAATACAAGCAGATCCCAGATGTAGATTACCTACAGgtactttttt ... ggtcatgaagGAGCTGCTGGCTATTCAGCAGCAAGGACCTCGTGCAATAGGTTTCTTTGGA
EST: gi|31363700|gb|CD448057.1|CD448057
EST:     CGGTTGCTGAACCAGAATACAAGCAGATCCCAGATGTAGATTACCTACAG                         GAGCTGCTGGCTATTCAGCAGCAAGGACCTCGTGCAATAGGTTTCTTTGGA
genomic: CGGTTGCTGAACCAGAATACAAGCAGATCCCAGATGTAGATTACCTACAGgtactttttt ... ggtcatgaagGAGCTGCTGGCTATTCAGCAGCAAGGACCTCGTGCAATAGGTTTCTTTGGA
EST: gi|74241321|gb|DT649235.1|DT649235
EST:     CGGTTGCTGAACCAGAATACAAGCAGATCCCAGATGTAGATTACCTACAG                         GAGCTGCTGGCTATTCAGCAGCAAGGACCTCGTGCAATAGGTTTCTTTGGA
genomic: CGGTTGCTGAACCAGAATACAAGCAGATCCCAGATGTAGATTACCTACAGgtactttttt ... ggtcatgaagGAGCTGCTGGCTATTCAGCAGCAAGGACCTCGTGCAATAGGTTTCTTTGGA
EST: gi|71445741|gb|DR826791.1|DR826791
EST:     CGGTTGCTGAACCAGAATACAAGCAGATCCCAGATGTAGATTACCTACAG                         GAGCTGCTGGCTATTCAGCAGCAAGGACCTCGTGCAATAGGTTTCTTTGGA
genomic: CGGTTGCTGAACCAGAATACAAGCAGATCCCAGATGTAGATTACCTACAGgtactttttt ... ggtcatgaagGAGCTGCTGGCTATTCAGCAGCAAGGACCTCGTGCAATAGGTTTCTTTGGA
EST: gi|149090139|gb|EE179439.2|EE179439
EST:     AGCAGATCCCAGATGTAGATTACCTACAG                         GAGCTGCTGGCTATTCAGCAGCAAGGACCTCGTGCAATAGGTTTCTTTGGA
genomic: AGCAGATCCCAGATGTAGATTACCTACAGgtactttttt ... ggtcatgaagGAGCTGCTGGCTATTCAGCAGCAAGGACCTCGTGCAATAGGTTTCTTTGGA
EST: gi|7844593|gb|AW787815.1|AW787815
EST:     CGGTTGCTGAACCAGAATACAAGCAGATCCCAGATGTAGATTACCTACAG                         GAGCTGCTGGCTATTCAGCAGC
genomic: CGGTTGCTGAACCAGAATACAAGCAGATCCCAGATGTAGATTACCTACAGgtactttttt ... ggtcatgaagGAGCTGCTGGCTATTCAGCAGC
EST: gi|76911678|gb|DV164374.1|DV164374
EST:     CGGTTGCTGAACCAGAATACAAGCAGATCCCAGATGTAGATTACCTACAG                         GAGCTGCTGGCTATTCAGCAGCAAGGACCTCGTGCAATAGGTTTCTTTGGA
genomic: CGGTTGCTGAACCAGAATACAAGCAGATCCCAGATGTAGATTACCTACAGgtactttttt ... ggtcatgaagGAGCTGCTGGCTATTCAGCAGCAAGGACCTCGTGCAATAGGTTTCTTTGGA
EST: gi|148973267|gb|EE024347.2|EE024347
EST:     CGGTTGCTGAACCAGAATACAAGCAGATCCCAGATGTAGATTACCTACAG                         GAGCTGCTGGCTATTCAGCAGCAAGGACCTCGTGCAATAGGTTTCTTTGGA
genomic: CGGTTGCTGAACCAGAATACAAGCAGATCCCAGATGTAGATTACCTACAGgtactttttt ... ggtcatgaagGAGCTGCTGGCTATTCAGCAGCAAGGACCTCGTGCAATAGGTTTCTTTGGA
EST: gi|71445740|gb|DR826790.1|DR826790
EST:     CGGTTGCTGAACCAGAATACAAGCAGATCCCAGATGTAGATAACCTACAG                         GAGCTGCTGGCTA
genomic: CGGTTGCTGAACCAGAATACAAGCAGATCCCAGATGTAGATTACCTACAGgtactttttt ... ggtcatgaagGAGCTGCTGGCTA
EST: gi|149014320|gb|EE043899.2|EE043899
EST:     CGGTTGCTGAACCAGAATACAAGCAGATCCCAGATGTAGATTACCTACAG                         GAGCTGCTGGCTATTCAGCAGCAAGGACCTCGTGCAATAGGTTTCTTTGGA
genomic: CGGTTGCTGAACCAGAATACAAGCAGATCCCAGATGTAGATTACCTACAGgtactttttt ... ggtcatgaagGAGCTGCTGGCTATTCAGCAGCAAGGACCTCGTGCAATAGGTTTCTTTGGA
EST: gi|71421265|gb|DR805363.1|DR805363
EST:     CGGTTGCTGAACCAGAATACAAGCAGATCCCAGATGTAGATTACCTACAG                         GAGCTGCTGGCTATTCAGCAGCAAGGACCTCGTGCAATAGGTTTCTTTGGA
genomic: CGGTTGCTGAACCAGAATACAAGCAGATCCCAGATGTAGATTACCTACAGgtactttttt ... ggtcatgaagGAGCTGCTGGCTATTCAGCAGCAAGGACCTCGTGCAATAGGTTTCTTTGGA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ctttatgaattgatttatcctatgaagtggactcatttattttgtggtcatgaagGAGCTGCTGGCTATTCAGCAGCAAGGACCTCGTGCAATAGGTTTCTTTGGAACCCGCAACATGGGATTTATGCACCAACAGCTTATTGAGATCCTGAGCT
       aattgat  putative branch site (score: 4)
       aattgatttat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtacttttttctgatcattttatactgaactgtttttttattaaaatttaagtttaatggttcttaaacctttcaaagttggtgtgatacaatcagaaatccaataatgaatgctacttagcatgtatgagctttatgaattgatttatcctatgaagtggactcatttattttgtggtcatgaagGAGCTGCTGGCTATTCAGCAGCAAGGACCTCGTGCAATAGGTTTCTTTGGAACCCGCAACATGGGATTTATGCACCAACAGCTTATTGAGATCCTGAGCT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGATC