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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtttgatgctccccttcatcattgtactaaaaattctgtagtgctatctagtaatagcagtttttatgacttctgtacgcttacggtgattttaattctattaccagCTTCTCCTTGTGGACAAGAAAATTAACAATGCCAGAGATCTTATCACTATCCTGGAGGATGCTATTAGAAGTGGATATCCAATTCTAATAGTGGCAGAGG

Basic information

species Zea mays
transcript GRMZM2G015989_T01
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G015989_T01 (Zea mays), 3'ss of exon 6
lower sequence: LOC_Os02g01280.1 (Oryza sativa), 3'ss of exon 6
gtttgatgctccccttcat-cattgtactaaaaattctgtagtgctatctagtaatagcagtttttatgacttctgtacgctt-acggtgattttaattctattacc-agCTTCTCCTTGTGGACAAGAAAATTAACAATGCCAGAGATCTTATCACTATCCTGGAGGATGCTATTAGAAGTGGATATCCAATTCTAATAGTGGCAGAGG
|||||||||   |    || |  |||||| |||   |||| |   || | ||  |||    |||   ||   ||| | |  || | | | || || ||||||| ||| || | |||||||||||||||||||| |||||||||||||||||||| || || |||||||||||||||||  |||| || ||||| ||||||||  | ||||
gtttgatgcattctagaattcggtgtacttaaa---ctgt-gcattaaccag--atactcattt--gtgggctctatgcatttgatgctaatgttgattctatcacccagTTGCTCCTTGTGGACAAGAAAATCAACAATGCCAGAGATCTTATAACAATTCTGGAGGATGCTATTAGGGGTGGGTACCCAATCCTAATAGTTACGGAGG

upper sequence: GRMZM2G015989_T01 (Zea mays), 3'ss of exon 6
lower sequence: GLYMA15G40110.1 (Glycine max), 3'ss of exon 5
gtttgatgctccccttcatcattgtactaaaaattctgtagtgctatctagtaatagcagtttttatgacttctgtacgcttacggtgattttaattctattaccagCTTCTCCTTGTGGACAAGAAAATTAACAATGCCAGAGATCTTATCACTATCCTGGAGGATGCTATTAGAAGTGGATATCCAATTCTAATAGTGGCAGAGG
      ||   |  ||     || | |    || |   || |  | | ||  |       | ||||       | ||   ||||  || |    ||  |||   ||| | ||  | || ||||| || || | |||||| || ||||||||||  || |||||||||||||||||||||||||| || ||  ||||  | || ||||
-----gtgtgacatttgtctgttttccctgtaacttgttattattttttaacatccttcatatttaa-----ttataactttaca-tggt----atgttat--gcagTTGCTGTTAGTTGACAAAAAGATAACCAATGCAAGGGATCTTATCAACATACTGGAGGATGCTATTAGAAGTGGATACCCTATATTAATTATTGCTGAGG

upper sequence: GRMZM2G015989_T01 (Zea mays), 3'ss of exon 6
lower sequence: GLYMA08G18760.2 (Glycine max), 3'ss of exon 5
gtttgatgctccccttcatcattgtactaaaaattctgtagtgctatctagtaatagcagtttttatgacttctgtacgcttacg-gtgatttta---attctattac-cagCTTCTCCTTGTGGACAAGAAAATTAACAATGCCAGAGATCTTATCACTATCCTGGAGGATGCTATTAGAAGTGGATATCCAATTCTAATAGTGGCAGAGG
                            | | |||     ||  |  ||   |||     |||||     | ||||    ||||   |   ||||     | | |||  ||| | ||  | || ||||| || || | ||||||  | ||||||||||  || |||||||||||||||||||||||| | || ||  | ||  | || ||||
-------------------------gtgagacatttgtctgttttccctgcgaattattattttttaacatcctgtgtatttacttatagctttatatggtatgttatgcagTTGCTGTTAGTTGACAAAAAGATAACCAATGCACGGGATCTTATCAACATACTGGAGGATGCTATTAGAAGTGGACACCCTATATTGATTATTGCTGAGG

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|32930585|gb|CF035397.1|CF035397
EST:     ACTTTGTGACTGACAGTGAAAAAATGACAGTCGAGTATGAGAACTGCAAG                         CTTCTCCTTGTGGACAAGAAAATTAACAATGCCAGAGATCTTATCACTATC
genomic: ACTTTGTGACTGACAGTGAAAAAATGACAGTCGAGTATGAGAACTGCAAGgtttgatgct ... ctattaccagCTTCTCCTTGTGGACAAGAAAATTAACAATGCCAGAGATCTTATCACTATC
EST: gi|31355200|gb|CD439557.1|CD439557
EST:     ACTTTGTGACTGACAGTGAAAAAATGACAGTCGAGTATGAGAACTGCCAG                         CTTCTCCTTGTGGA
genomic: ACTTTGTGACTGACAGTGAAAAAATGACAGTCGAGTATGAGAACTGCAAGgtttgatgct ... ctattaccagCTTCTCCTTGTGGA
EST: gi|211451955|gb|FL157391.1|FL157391
EST:     ACTTTGTGACTGACAGTGAAAAAATGACAGTCGAGTATGAGAACTGCAAG                         CTTCTCCTTGTGGACAAGAAAATTAACAATGCCAGAGATCTTATCACTATC
genomic: ACTTTGTGACTGACAGTGAAAAAATGACAGTCGAGTATGAGAACTGCAAGgtttgatgct ... ctattaccagCTTCTCCTTGTGGACAAGAAAATTAACAATGCCAGAGATCTTATCACTATC
EST: gi|211451956|gb|FL157392.1|FL157392
EST:     ACTTTGTGACTGACAGTGAAAAAATGACAGTCGAGTATGAGAACTGCAAG                         CTTCTCCTTGTGGAC
genomic: ACTTTGTGACTGACAGTGAAAAAATGACAGTCGAGTATGAGAACTGCAAGgtttgatgct ... ctattaccagCTTCTCCTTGTGGAC
EST: gi|211451954|gb|FL157390.1|FL157390
EST:     ACTTTGTGACTGACAGTGAAAAAATGACAGTCGAGTATGAGAACTGCAAG                         CTTCTCCTTGTGGACAAGAAAATTAACAATGCCAGAGATCTTATCACTATC
genomic: ACTTTGTGACTGACAGTGAAAAAATGACAGTCGAGTATGAGAACTGCAAGgtttgatgct ... ctattaccagCTTCTCCTTGTGGACAAGAAAATTAACAATGCCAGAGATCTTATCACTATC
EST: gi|78081967|gb|DV510379.1|DV510379
EST:     ACTTTGTGACTGACAGTGAAAAAATGACAGTCGAGTATGAGAACTGCAAG                         CTTCTCCTTGTGGACAAGAAAATTAACAATGCCAGAGATCTTATCACTATC
genomic: ACTTTGTGACTGACAGTGAAAAAATGACAGTCGAGTATGAGAACTGCAAGgtttgatgct ... ctattaccagCTTCTCCTTGTGGACAAGAAAATTAACAATGCCAGAGATCTTATCACTATC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aatagcagtttttatgacttctgtacgcttacggtgattttaattctattaccagCTTCTCCTTGTGGACAAGAAAATTAACAATGCCAGAGATCTTATCACTATCCTGGAGGATGCTATTAGAAGTGGATATCCAATTCTAATAGTGGCAGAGG
                                     ttttaat  putative branch site (score: 3)
                                           ttctatt  CT-rich tract
                                  tgattttaattctatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtttgatgctccccttcatcattgtactaaaaattctgtagtgctatctagtaatagcagtttttatgacttctgtacgcttacggtgattttaattctattaccagCTTCTCCTTGTGGACAAGAAAATTAACAATGCCAGAGATCTTATCACTATCCTGGAGGATGCTATTAGAAGTGGATATCCAATTCTAATAGTGGCAGAGG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAAGT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGTGGA