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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtcagctttttattagtgaaaattgtatttatttacttcatctgcagttctgttttctgacatcatgcataatatttgaggaaacgccagTCTATCCTGATGGGCGGGTTTGTATCTCTATTCTTCATCCACCTGGTGAAGATCCAAACGGTTATGAGCTCGCAAGTGAGCGATGGACACCTGTGCACAC

Basic information

species Zea mays
transcript GRMZM2G085600_T03
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G085600_T03 (Zea mays), 3'ss of exon 3
lower sequence: LOC_Os01g62244.3 (Oryza sativa), 3'ss of exon 1
gtcagctttttattagtgaaaattgtatttatttacttcatctgcagttctgttttctgacatcatgcataatatttgaggaaacgccagTCTATCCTGATGGGCGGGTTTGTATCTCTATTCTTCATCCACCTGGTGAAGATCCAAACGGTTATGAGCTCGCAAGTGAGCGATGGACACCTGTGCACAC
|||||||||   | | || || ||  || | | |    | ||     | |    || | |||    |||||||||| |   ||  |||||| ||||| ||||| || || || || |||||||||||||| |||||||| ||||| || ||||||||||| || |||||||| |||||||| ||||| ||
gtcagctttcc-tcattgtaactt-catgtttctgtaac-tccatgatccataattttaacaca--gcataatatt-ggtcaattgccagTTTATCCGGATGGACGTGTATGCATTTCTATTCTTCATCCGCCTGGTGATGATCCCAATGGTTATGAGCTTGCGAGTGAGCGTTGGACACCAGTGCATAC

upper sequence: GRMZM2G085600_T03 (Zea mays), 3'ss of exon 3
lower sequence: GLYMA12G06960.1 (Glycine max), 3'ss of exon 3
gtcagctttttattagtgaaaattgtatttatttacttcatctgcagttctgttttctgacatcatgcataatatttgaggaaacgccagTCTATCCTGATGGGCGGGTTTGTATCTCTATTCTTCATCCACCTGGTGAAGATCCAAACGGTTATGAGCTCGCAAGTGAGCGATGGACACCTGTGCACAC
|| ||  |||| || |   || ||||  || ||   || || || | | |       |||  |  |   |   ||||  |       |||| ||||| ||||| |||||||| || || ||||||||||| |||||||| |||||||| ||||| ||||| || |||||||| ||||||||||| || ||
gttagtgttttttttg---aatttgtgatt-ttgctttgatttgaactacatgaaagtgatgttttctgttcaatttttg-------cagTATATCCCGATGGCCGGGTTTGCATATCAATTCTTCATCCTCCTGGTGAGGATCCAAATGGTTACGAGCTTGCGAGTGAGCGCTGGACACCTGTTCATAC

upper sequence: GRMZM2G085600_T03 (Zea mays), 3'ss of exon 3
lower sequence: GLYMA15G04470.2 (Glycine max), 3'ss of exon 3
gtcagctttttattagtgaaaattgtatttatttacttcatctgcagttctgttttctgacatcatgcataatatttgaggaaacgccagTCTATCCTGATGGGCGGGTTTGTATCTCTATTCTTCATCCACCTGGTGAAGATCCAAACGGTTATGAGCTCGCAAGTGAGCGATGGACACCTGTGCACAC
            || ||     |  | |||||||   || |     | | || |   ||| |  ||| || ||  | |    |    |||| || || |||||||| ||||| || || |||||||||||||| ||||| || ||||| ||||||||||| ||||||||||| ||||| ||||| || ||
-----------gttggtttggctcatttttatttttatcttgctttgat-tgatacatgata--atgaatgatgct-gttccatttgcagTGTACCCCGATGGGCGAGTTTGCATATCAATTCTTCATCCACCCGGTGATGACCCAAATGGTTATGAGCTTGCAAGTGAGCGCTGGACGCCTGTTCATAC

upper sequence: GRMZM2G085600_T03 (Zea mays), 3'ss of exon 3
lower sequence: GLYMA11G14980.1 (Glycine max), 3'ss of exon 3
gtcagctttttattagtgaaaattgtatttatttacttcatctgcagttctgttttctgacatcatgcataatatttgaggaaacgc--cagTCTATCCTGATGGGCGGGTTTGTATCTCTATTCTTCATCCACCTGGTGAAGATCCAAACGGTTATGAGCTCGCAAGTGAGCGATGGACACCTGTGCACAC
|| || ||||| ||  | ||  ||||  ||  || |||     | |      |     |  ||||   ||  |   ||   ||      |||| ||||||||||| |||||||| || || ||||||||||| |||||||| |||||||| ||||||||||| ||||||||||| ||||||||||| || ||
gttagtttttttttttttaat-ttgtgatt--ttgctttgataggaacaacatgaaa-gtgatcagtgatgtttcctgttcaatttttgcagTATATCCTGATGGCCGGGTTTGCATATCAATTCTTCATCCTCCTGGTGAGGATCCAAATGGTTATGAGCTTGCAAGTGAGCGCTGGACACCTGTTCATAC

upper sequence: GRMZM2G085600_T03 (Zea mays), 3'ss of exon 3
lower sequence: GLYMA13G40990.1 (Glycine max), 3'ss of exon 3
gtcagctttttattagtgaaaattgtatttatttacttcatctgcagttctgttttctgacatcatgcataatatttgaggaaacgccagTCTATCCTGATGGGCGGGTTTGTATCTCTATTCTTCATCCACCTGGTGAAGATCCAAACGGTTATGAGCTCGCAAGTGAGCGATGGACACCTGTGCACAC
            || ||   |     |||| |||  | |  || |  |  |  |   ||| ||  |  || || || |   ||    |||| |||||||||||||| ||||| || || ||||||||||| |||||||| || ||||| ||||||||||| ||||||||||| ||||| ||||| || ||
-----------gttggtctga--cacattttttttatcctgcttcgat--taatacatgaaat--tcaatgatgtt-gttcaatttgcagTGTATCCTGATGGGCGAGTTTGCATATCAATTCTTCATCCTCCTGGTGACGACCCAAATGGTTATGAGCTTGCAAGTGAGCGCTGGACGCCTGTTCATAC

upper sequence: GRMZM2G085600_T03 (Zea mays), 3'ss of exon 3
lower sequence: AT3G46460.1 (Arabidopsis thaliana), 3'ss of exon 3
gtcag--ctttttattagtgaaaattgtatttatttacttcatctgcagttctgttttctgacatcatgc-ataatatttga---ggaaacgccagTCTATCCTGATGGGCGGGTTTGTATCTCTATTCTTCATCCACCTGGTGAAGATCCAAACGGTTATGAGCTCGCAAGTGAGCGATGGACACCTGTGCACAC
|| ||  |||| | |  || |       |||   | | || ||||   |||    |  || |  |  ||  | ||| || |    |    |  |||| ||||| ||||| || |||||||| |||||||| ||||| |||||||| |||||||  || |||||||| ||||||||||| ||||| ||||| |||||
gttagttctttctctcggttatgcgctcattagctca-ttgatctt--gtttgagtagctaaggttttgtgaaaatgttcgtcttgtggtctgcagTTTATCCCGATGGCCGCGTTTGTATATCTATTCTACATCCTCCTGGTGATGATCCAAGTGGATATGAGCTTGCAAGTGAGCGTTGGACGCCTGTTCACAC

upper sequence: GRMZM2G085600_T03 (Zea mays), 3'ss of exon 3
lower sequence: AT5G59300.1 (Arabidopsis thaliana), 3'ss of exon 3
---------------gtcagctttttattagtgaaaattgtatttatttacttcatctgcagttctgttttctgacatcatgcataatatttgaggaaacgccagTCTATCCTGATGGGCGGGTTTGTATCTCTATTCTTCATCCACCTGGTGAAGATCCAAACGGTTATGAGCTCGCAAGTGAGCGATGGACACCTGTGCACAC
                || | |||| ||  | |||   |  |      ||  | |   | ||       ||   |     | | || ||||||      |  |||| ||| ||||||| || ||||| || |||||||||||||| || ||||| ||||| | |||||||||||| ||||| ||||| ||||| ||||| || ||
gttagttttctctctatcgg-ttttgatcggggaaggattcaaaggaata--tgaatagaagacagacgtttgaatggtttactta-tatttgt----cctgcagTTTATTCTGATGGTCGTGTTTGCATATCTATTCTTCATCCTCCCGGTGATGATCCTAGCGGTTATGAGCTTGCAAGCGAGCGTTGGACTCCTGTTCATAC

upper sequence: GRMZM2G085600_T03 (Zea mays), 3'ss of exon 3
lower sequence: Vv08s0007g00120.t01 (Vitis vinifera), 3'ss of exon 3
gtcagctttttattagtgaaaattgtatttatttacttcatctgcagttctg----ttttctgacatcatgcataatatttgaggaaacgccagTCTATCCTGATGGGCGGGTTTGTATCTCTATTCTTCATCCACCTGGTGAAGATCCAAACGGTTATGAGCTCGCAAGTGAGCGATGGACACCTGTGCACAC
|| | ||| ||||   |   |  |  || ||| ||  | |  | |   |  |     | |||||    |    ||     |    ||||  |||| ||||||||||| || ||||| || || ||| | ||||| |||||||| || ||||| || |||||||| ||||||||||| ||||||||||| |||||
gttaacttcttatgcctctcatatacatatatatatatgaatttctcattggagcactctctgatgctaattgtacctacttcttaaactgcagTTTATCCTGATGGACGAGTTTGCATATCAATTTTACATCCTCCTGGTGAGGACCCAAATGGCTATGAGCTTGCAAGTGAGCGTTGGACACCTGTCCACAC

upper sequence: GRMZM2G085600_T03 (Zea mays), 3'ss of exon 3
lower sequence: Vv06s0004g04430.t01 (Vitis vinifera), 3'ss of exon 3
gtcagctttttatt--agtgaaaat-tgtatttatttacttcatctgcagttctgttttctgacatcatgcataatatttgaggaaacgccagTCTATCCTGATGGGCGGGTTTGTATCTCTATTCTTCATCCACCTGGTGAAGATCCAAACGGTTATGAGCTCGCAAGTGAGCGATGGACACCTGTGCACAC
||  | | ||| |   | || |  | | |  || || |||    |    |     |    ||| ||||  | |  |  |||    ||   |||| ||||| ||||| || || || || || ||||| ||||| |||||||| || ||||| || |||||||| ||||||||||| ||||  ||  | || ||
gttggttgtttgtccaactgcatgtgtttgatttttgactcttaccattggagcatggcttgaaatca-acttggttcttgcatgaattacagTTTATCCAGATGGACGAGTATGCATATCAATTCTCCATCCTCCTGGTGAGGACCCAAATGGATATGAGCTTGCAAGTGAGCGCTGGATGCCAATCCATAC

upper sequence: GRMZM2G085600_T03 (Zea mays), 3'ss of exon 3
lower sequence: PP1S75_236V6.1 (Physcomitrella patens), 3'ss of exon 5
--gtcagctttttattagtgaaaattgtatttattt-acttcatctgcagttctgtt-ttctgacatcatgcata---atatttgaggaaacgc---cagTCTATCCTGATGGGCGGGTTTGTATCTCTATTCTTCATCCACCTGGTGAAGATCCAAACGGTTATGAGCTCGCAAGTGAGCGATGGACACCTGTGCACAC
     | || |   ||       | || | | || | |||| || |    ||  | | |||||      | ||||   ||  ||||     |     |||| ||||||||||| |||||||| || || ||||| ||| | |||||||| |||||||| ||||||||  | || |||||||| ||| | || ||||| ||
gaaagaactctggtttgactctgaatgcactcatgtgacttaatttttctttacgatgttctgcttatttccataccaatccttgacttttcatgtgcagTTTATCCTGATGGACGGGTTTGCATTTCAATTCTACATGCTCCTGGTGATGATCCAAATGGTTATGAATTGGCGAGTGAGCGTTGGTCTCCCGTGCATAC

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|211533490|gb|FK952750.1|FK952750
EST:     AAACAGCCCGCCATCAGTCAGATTTACCTCTGAAATGTGGCATCCAAATG                         TCTATCCTGATGGGCGGGTTTGTATCTCTATTCTTCATCCACCTGGTGAAG
genomic: AAACAGCCCGCCATCAGTCAGATTTACCTCTGAAATGTGGCATCCAAATGgtcagctttt ... gaaacgccagTCTATCCTGATGGGCGGGTTTGTATCTCTATTCTTCATCCACCTGGTGAAG
EST: gi|211533484|gb|FK952744.1|FK952744
EST:     AAACAGCCCGCCATCAGTCAGATTTACCTCTGAAATGTGGCATCCAAATG                         TCTATCCTGATGGGCGGGTTTGTATCTCTATTCTTCATCCACCTGGTGAAG
genomic: AAACAGCCCGCCATCAGTCAGATTTACCTCTGAAATGTGGCATCCAAATGgtcagctttt ... gaaacgccagTCTATCCTGATGGGCGGGTTTGTATCTCTATTCTTCATCCACCTGGTGAAG
EST: gi|211533493|gb|FK952753.1|FK952753
EST:     AAACAGCCCGCCATCAGTCAGATTTACCTCTGAAATGTGGCATCCAAATG                         TCTATCCTGATGGGCGGGTTTGTATCTCTATTCTTCATCCACCTGGTGAAG
genomic: AAACAGCCCGCCATCAGTCAGATTTACCTCTGAAATGTGGCATCCAAATGgtcagctttt ... gaaacgccagTCTATCCTGATGGGCGGGTTTGTATCTCTATTCTTCATCCACCTGGTGAAG
EST: gi|211530484|gb|FK952736.1|FK952736
EST:     AAACAGCCCGNCATCAGTCAGATTTACCTCTGAAATGTGGCATCCAAATG                         TCTATCCTGATGG
genomic: AAACAGCCCGCCATCAGTCAGATTTACCTCTGAAATGTGGCATCCAAATGgtcagctttt ... gaaacgccagTCTATCCTGATGG
EST: gi|211313830|gb|FL083564.1|FL083564
EST:     AAACAGCCCGCCATCAGTCAGATTTACCTCTGAAATGTGGCATCCAAATG                         TCTATCCTGATGGGCAGGTTTGTATCTCTATTCTTCATCCACCTGGTGAAG
genomic: AAACAGCCCGCCATCAGTCAGATTTACCTCTGAAATGTGGCATCCAAATGgtcagctttt ... gaaacgccagTCTATCCTGATGGGCGGGTTTGTATCTCTATTCTTCATCCACCTGGTGAAG
EST: gi|211533486|gb|FK952746.1|FK952746
EST:     AAACAGCCCGCCATCAGTCAGATTTACCTCTGAAATGTGGCATCCAAATG                         TCTATCCTGATGGGCGGGTTTGTATCTCTATTCTTCATCCACCTGGT
genomic: AAACAGCCCGCCATCAGTCAGATTTACCTCTGAAATGTGGCATCCAAATGgtcagctttt ... gaaacgccagTCTATCCTGATGGGCGGGTTTGTATCTCTATTCTTCATCCACCTGGT
EST: gi|211315846|gb|FL083573.1|FL083573
EST:     AAACAGCCCGCCATCAGTCAGATTTACCTCTGAAATGTGGCATCCAAATG                         TCTATCCTGATGGGCAGGTTTGTATCTCTATTCTTCATCCACCTGGTGAAG
genomic: AAACAGCCCGCCATCAGTCAGATTTACCTCTGAAATGTGGCATCCAAATGgtcagctttt ... gaaacgccagTCTATCCTGATGGGCGGGTTTGTATCTCTATTCTTCATCCACCTGGTGAAG
EST: gi|211530487|gb|FK952739.1|FK952739
EST:     AAACAGCCCGCCATCAGTCAGATTTACCTCTGAAATGTGGCATCCAAATG                         TCTATCCTGATGGGCGGGTTTGTATCTCTATTCTTCATCCACCTGGTGAAG
genomic: AAACAGCCCGCCATCAGTCAGATTTACCTCTGAAATGTGGCATCCAAATGgtcagctttt ... gaaacgccagTCTATCCTGATGGGCGGGTTTGTATCTCTATTCTTCATCCACCTGGTGAAG
EST: gi|74240335|gb|DT648249.1|DT648249
EST:     AAACAGCCCGCCATCAGTCAGATTTACCTCTGAAATGTGGCATCCAAATG                         TCTATCCTGATGGGCGGGTTTGTATCTCTATTCTTCATCCACCTGGTGAAG
genomic: AAACAGCCCGCCATCAGTCAGATTTACCTCTGAAATGTGGCATCCAAATGgtcagctttt ... gaaacgccagTCTATCCTGATGGGCGGGTTTGTATCTCTATTCTTCATCCACCTGGTGAAG
EST: gi|211530485|gb|FK952737.1|FK952737
EST:     AAACAGCCCGCCATCAGTCAGATTTACCTCTGAAATGTGGCATCCAAATG                         TCTATCCTGATGGGCGGGTTTGTATCTCTATTCTTCATCCACCTGGTGAAG
genomic: AAACAGCCCGCCATCAGTCAGATTTACCTCTGAAATGTGGCATCCAAATGgtcagctttt ... gaaacgccagTCTATCCTGATGGGCGGGTTTGTATCTCTATTCTTCATCCACCTGGTGAAG
EST: gi|211533485|gb|FK952745.1|FK952745
EST:     AAACAGCCCGCCATCAGTCAGATTTACCTCTGAAATGTGGCATCCAAATG                         TCTATCCTGATGGGCGGGTTTGTATCTCTATTCTTCATCCACCTGGTGAAG
genomic: AAACAGCCCGCCATCAGTCAGATTTACCTCTGAAATGTGGCATCCAAATGgtcagctttt ... gaaacgccagTCTATCCTGATGGGCGGGTTTGTATCTCTATTCTTCATCCACCTGGTGAAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cttcatctgcagttctgttttctgacatcatgcataatatttgaggaaacgccagTCTATCCTGATGGGCGGGTTTGTATCTCTATTCTTCATCCACCTGGTGAAGATCCAAACGGTTATGAGCTCGCAAGTGAGCGATGGACACCTGTGCACAC
                   ttctgac  putative branch site (score: 2)
                                 ataatatttga  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtcagctttttattagtgaaaattgtatttatttacttcatctgcagttctgttttctgacatcatgcataatatttgaggaaacgccagTCTATCCTGATGGGCGGGTTTGTATCTCTATTCTTCATCCACCTGGTGAAGATCCAAACGGTTATGAGCTCGCAAGTGAGCGATGGACACCTGTGCACAC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GATGGA