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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtacattgctcccatgttggaccctatacattttgcagcaagtaatttgctttctttgtggatatattattgggagacatgtttttagttgctagaggttgataatttctcggagtcgcctcttagttttgcaacttgctgcagttcagtgcattaccgctgataaatgctacttgcatatactcgctttgtttagGATAAATCATGGCGTGTTCGTTATATGGTCGCCAATCAGTTATATGAGCTCTGTGAGGCTGTTGGCCCTGAGCCCACAAG

Basic information

species Zea mays
transcript GRMZM2G122135_T04
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G122135_T01 (Zea mays), 3'ss of exon 4
lower sequence: GLYMA09G31760.1 (Glycine max), 3'ss of exon 4
gtacattgctcccatgttggaccctatacattttgcagcaagtaatttgctttctttgtggatatattattgggagacatgtttttagttgctagaggttgataatttctcggagtcgcctcttagttttgcaacttgctgcagttcagtgcattaccgctgataaatgctacttgcatatactcgctttgtttagGATAAATCATGGCGTGTTCGTTATATGGTCGCCAATCAGTTATATGAGCTCTGTGAGGCTGTTGGCCCTGAGCCCACAAG
                                                                                      || | |         |||||||  |    | ||    |||| ||||   || |   | |  ||| |   |    ||  | ||  ||   | || ||||    || |  ||||||| ||||||||||||||||| ||||| || |||||  |||||||||| ||||| |||||||| ||||| ||||| ||
------------------------------------------------------------------------------------aaagatacatagaaaaaataattttgctt--ttgctgtctagtattgc---ttccaaaaatgaagttctacatt-ttgtcacatagta---gaat-tact--tcttatccagGATAAGTCATGGCGTGTTCGTTACATGGTTGCTAATCAACTATATGAGCTATGTGAAGCTGTTGGTCCTGACCCCACCAG

upper sequence: GRMZM2G122135_T01 (Zea mays), 3'ss of exon 4
lower sequence: GLYMA07G10000.1 (Glycine max), 3'ss of exon 3
gtacattgctcccatgttggaccctatacattttgcagcaagtaatttgctttctttgtggatatattattgggagacatgtttttagttgctagaggttgataatttctcggagtcgcctcttagttttgcaacttgctgcagttcagtgcattaccgctgataaatgc-tacttgcatatactcgctttgtttagGATAAATCATGGCGTGTTCGTTATATGGTCGCCAATCAGTTATATGAGCTCTGTGAGGCTGTTGGCCCTGAGCCCACAAG
                                                                                             | || |  |||         | |   || ||    |      ||||| |     | || ||| |  |   |     | || ||| || ||||    || |  ||||||| ||||||||||||||||| ||||| || |||||  |||||||||| ||||| |||||||| ||||| ||||| ||
---------------------------------------------------------------------------------------------aaagttacatagaaaaattaattttgcttttgccgtcttgtattgcttcgaaa-aatgaatttctacatcttgtcacatagttgaat-tact--tcttatccagGATAAGTCATGGCGTGTTCGTTACATGGTTGCTAATCAACTATATGAGCTATGTGAAGCTGTTGGTCCTGACCCCACCAG

upper sequence: GRMZM2G122135_T01 (Zea mays), 3'ss of exon 4
lower sequence: Vv17s0000g03870.t01 (Vitis vinifera), 3'ss of exon 5
gtacattgctcccatgttggaccctatacattttgcagcaagtaatttgctttctttgtggatatattattgggagacatgtttttagttgctagaggttgataatt-tctcggagtcgcctcttagttttgcaacttgctgcagttcagtgcattaccgctgataaatgctacttgcatatactcgctttgtttagGATAAATCATGGCGTGTTCGTTATATGGTCGCCAATCAGTTATATGAGCTCTGTGAGGCTGTTGGCCCTGAGCCCACAAG
                                                                             ||   |  ||    |||  |  | |||||| ||    |      |   ||| |  |||  ||     ||| | |  || |  |   || |    |  || | |  ||           ||||||| || ||||||||||| |||||||| || ||||| ||||||||||| ||||| |||||||| |||||||| || ||
-----------------------------------------------------------------------------caaactcata----ctattgagtcataattctcataaaaatagttagaagtgtcacaatatg-----gtttatttgatcattgtgtatgagaaattttttcctgaac-----------agGATAAGTCTTGGCGTGTTCGCTATATGGTTGCAAATCAATTATATGAGCTATGTGAAGCTGTTGGTCCTGAGCCTACCAG

upper sequence: GRMZM2G122135_T01 (Zea mays), 3'ss of exon 4
lower sequence: Vv03s0038g00200.t01 (Vitis vinifera), 3'ss of exon 1
gtacattgctcccatgttggaccctatacattttgcagcaagtaatttgctttctttgtggatatattattgggagacatgtttttagttgctagaggttgataatttctcggagtcgcctcttagttttgcaacttgctgcagttcagtgcattaccgctgataaatgctacttgcatatactc---gctttgtttagGATAAATCATGGCGTGTTCGTTATATGGTCGCCAATCAGTTATATGAGCTCTGTGAGGCTGTTGGCCCTGAGCCCACAAG--------------------
                                                                                                                                                                |   | ||  |  |  |||| | |      ||   | ||||||| || ||||||||||| |||||||| || ||||| ||||||||||| ||||| |||||||| |||||||| || ||                    
---------------------------------------------------------------------------------------------------------------------------------------------------------------gtagcacatattcttcccataaattatgaatttctctcagGATAAGTCTTGGCGTGTTCGCTATATGGTTGCAAATCAATTATATGAGCTATGTGAAGCTGTTGGTCCTGAGCCTACCAGGTCAGACTTGGTTCCTGCAT

upper sequence: GRMZM2G122135_T01 (Zea mays), 3'ss of exon 4
lower sequence: Vv04s0008g07090.t01 (Vitis vinifera), 3'ss of exon 2
gtacattgctcccatgttggaccctatacattttgcagcaagtaatttgctttctttgtggatatattattgggagacatgtttttagttgctagaggttgataatttctcggagtcgcctcttagttttgcaacttgctgcagttcagtg--cattaccgctgataaatgctacttgcatatactc---gctttgtttagGATAAATCATGGCGTGTTCGTTATATGGTCGCCAATCAGTTATATGAGCTCTGTGAGGCTGTTGGCCCTGAGCCCACAAG
                                                       |  | ||   |  | |  |  | |     || | | ||  ||  | ||| | | |  |       | ||  |  | |  |||  |  || | ||    ||| |        | ||  | ||  |||| | |      ||   | ||||||| || ||||||||||| |||||||| || ||||| ||||||||||| ||||| |                      
----------------------------------------------------cgatcctaga---accactatgctatagtagcttggctactttag--taatagtatttaaggtataaattttgttgatacgcctt--taaagctaagctaccatgagTCGCATCACATATTCCTCCCATAAATTATGAATTTCTCTCAGGATAAGTCTTGGCGTGTTCGCTATATGGTTGCAAATCAATTATATGAGCTATGTGAAG----------------------

upper sequence: GRMZM2G122135_T01 (Zea mays), 3'ss of exon 4
lower sequence: PP1S197_114V6.1 (Physcomitrella patens), 3'ss of exon 3
gtacattgctcccatgttggaccctatacattttgcagcaagtaatttgctttctttgtggatatattattgggagacatgtttttagttgctagaggttgataatttctcggagtcgcctcttagttttgcaacttgctgcagttcagtgcattaccgctgataaatgctacttgcatatactcgctttgttt-agGATAAATCATGGCGTGTTCGTTATATGGTCGCCAATCAGTTATATGAGCTCTGTGAGGCTGTTGGCCCTGAGCCCACAAG
                                                                                            |   | |  ||  | | || |||    | |   |  |      |   |  ||||   | ||| ||      |||||    | ||  | | |  |     ||  |||| ||||||||| | || || || ||||| ||||| |||||||||||||| |||||||| || || || || || || ||
--------------------------------------------------------------------------------------------ttctgttaaatcttctttcagagctaaccccagggatgttctttgagtatagttatatacat-acaataattaaat----catgagtttccctgtgggattccagGACAAATCATGGAGGGTACGATACATGGTGGCCAACCAGTTATATGAGCTTTGTGAGGCGGTAGGACCAGAACCAACCAG

upper sequence: GRMZM2G122135_T01 (Zea mays), 3'ss of exon 4
lower sequence: PP1S117_137V6.1 (Physcomitrella patens), 3'ss of exon 3
gtacattgctcccatgttggaccctatacattttgcagcaagtaatttgctttctttgtggatatattattgggagacatgtttttagttgctagaggttgataatttctcggagtcgcctcttagttttgcaacttgctgcagttcagtgcattaccg-ctgataaatgctacttgcatatactcgctttgtttagGATAAATCATGGCGTGTTCGTTATATGGTCGCCAATCAGTTATATGAGCTCTGTGAGGCTGTTGGCCCTGAGCCCACAAG
                                                                                                  |||  ||  |  | ||||  ||| |  | |||   ||   ||    |  | || |       || ||    | | || |  |      |   | |  |||| || ||||||||||||||||| ||||| || || ||||| || ||||| |||||||| || || || ||||| || ||
---------------------------------------------------------------------------------------------tctatttgggaagattccagagtt-cctatcggatttatcac--actaagttcaaatgtagagttatcttattttagtttctcgattgcctgtggact-tccagGACAAGTCATGGCGTGTTCGTTACATGGTAGCTAACCAGTTGTACGAGCTATGTGAGGCGGTCGGGCCAGAGCCTACCAG

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|32929087|gb|CF033899.1|CF033899
EST:     CACAAGATTGTGTAGCTCACATTCTTCCAGTCATTGTCAATTTCTCCCAG                         GATAAATCATGGCGTGTTCGTTATATGGTCGCCAATCAGTTATATGAGCTC
genomic: CACAAGATTGTGTAGCTCACATTCTTCCAGTCATTGTCAATTTCTCCCAGgtacattgct ... ctttgtttagGATAAATCATGGCGTGTTCGTTATATGGTCGCCAATCAGTTATATGAGCTC
EST: gi|6564198|gb|AW231820.1|AW231820
EST:     CACAAGATTGTGTAGCTCACATTCTTCCAGTCATTGTCAATTTCTCCCAG                         GATAAATCATGGCGTGTTCGTTATATGGTCGCCAATCAGTTATATGAGCTC
genomic: CACAAGATTGTGTAGCTCACATTCTTCCAGTCATTGTCAATTTCTCCCAGgtacattgct ... ctttgtttagGATAAATCATGGCGTGTTCGTTATATGGTCGCCAATCAGTTATATGAGCTC
EST: gi|31356310|gb|CD440667.1|CD440667
EST:     CACAAGATTGTGTAGCTCACATTCTTCCAGTCATTGTCAATTTCTCCCAG                         GATAAATCATGGCGTGTTCGTTATATGGTCGCCAATCAGTTATATGAGCTC
genomic: CACAAGATTGTGTAGCTCACATTCTTCCAGTCATTGTCAATTTCTCCCAGgtacattgct ... ctttgtttagGATAAATCATGGCGTGTTCGTTATATGGTCGCCAATCAGTTATATGAGCTC
EST: gi|5566949|gb|AI881860.1|AI881860
EST:     CACAAGATTGTGTAGCTCACATTCTTCCAGTCATTGTCAATTTCTCCCAG                         GATAAATCATGGCGTGTTCGTTATATGGTCGCCAATCAGTTATATGAGCTC
genomic: CACAAGATTGTGTAGCTCACATTCTTCCAGTCATTGTCAATTTCTCCCAGgtacattgct ... ctttgtttagGATAAATCATGGCGTGTTCGTTATATGGTCGCCAATCAGTTATATGAGCTC
EST: gi|67034361|gb|CO462911.1|CO462911
EST:     CACAAGATTGTGTAGCTCACATTCTTCCAGTCATTGTCAATTTCTCCCAG                         GATAAATCATGGCGTGTTCGTTATATGGTCGCCAATCAGTTATATGAGCTC
genomic: CACAAGATTGTGTAGCTCACATTCTTCCAGTCATTGTCAATTTCTCCCAGgtacattgct ... ctttgtttagGATAAATCATGGCGTGTTCGTTATATGGTCGCCAATCAGTTATATGAGCTC
EST: gi|24763712|gb|CA398883.1|CA398883
EST:     CACAAGATTGTGTAGCTCACATTCTTCCAGTCATTGTCAATTTCTCCCAG                         GATAAATCATGGCGTGTTCGTTATATGGTCGCCAATCAGTTATATGAGCTC
genomic: CACAAGATTGTGTAGCTCACATTCTTCCAGTCATTGTCAATTTCTCCCAGgtacattgct ... ctttgtttagGATAAATCATGGCGTGTTCGTTATATGGTCGCCAATCAGTTATATGAGCTC
EST: gi|13126723|gb|BG317293.1|BG317293
EST:     CACAAGATTGTGTAGCTCACATTCTTCCAGTCATTGTCAATTTCTCCCAG                         GATAAATCATGGCGTGTTCGTTATATGGTCGCCAATCAGTTATATGAGCTC
genomic: CACAAGATTGTGTAGCTCACATTCTTCCAGTCATTGTCAATTTCTCCCAGgtacattgct ... ctttgtttagGATAAATCATGGCGTGTTCGTTATATGGTCGCCAATCAGTTATATGAGCTC
EST: gi|14191183|gb|BG833413.1|BG833413
EST:     CACAAGATTGTGTAGCTCACATTCTTCCAGTCATTGTCAATTTCTCCCAG                         GATAAATCATGGCGTG
genomic: CACAAGATTGTGTAGCTCACATTCTTCCAGTCATTGTCAATTTCTCCCAGgtacattgct ... ctttgtttagGATAAATCATGGCGTG
EST: gi|21843193|gb|BQ703774.1|BQ703774
EST:     CACAAGATGGTGTAGCTCACATTCTTCCAGTCATTGTCAATTTCTCCCAG                         GATAAATCATG
genomic: CACAAGATTGTGTAGCTCACATTCTTCCAGTCATTGTCAATTTCTCCCAGgtacattgct ... ctttgtttagGATAAATCATG
EST: gi|20803006|gb|BQ294056.1|BQ294056
EST:     CACAAGATTGTGTAGCTCACATTCTTCCAGTCATTGTCAATTTCTCCCAG                         GATAAATCATGGCGTGTTCGTTATATGGTCGCCAATCAGTTATATGAGCTC
genomic: CACAAGATTGTGTAGCTCACATTCTTCCAGTCATTGTCAATTTCTCCCAGgtacattgct ... ctttgtttagGATAAATCATGGCGTGTTCGTTATATGGTCGCCAATCAGTTATATGAGCTC
EST: gi|32941448|gb|CF046267.1|CF046267
EST:     CACAAGATTGTGTAGCTCACATTCTTCCAGTCATTGTCAATTTCTCCCAG                         GATAAATCATGGCGTGTTCGTTATATGGTCGCCAATCAGTTATATGAGCTC
genomic: CACAAGATTGTGTAGCTCACATTCTTCCAGTCATTGTCAATTTCTCCCAGgtacattgct ... ctttgtttagGATAAATCATGGCGTGTTCGTTATATGGTCGCCAATCAGTTATATGAGCTC
EST: gi|13126316|gb|BG316886.1|BG316886
EST:     CACAAGATTGTGTAGCTCACATTCTTCCAGTCATTGTCAATTTCTCCCAG                         GATAAATCATGGCGTGTTCGTTATATGGTCGCCAATCAGCTATATGAGCTC
genomic: CACAAGATTGTGTAGCTCACATTCTTCCAGTCATTGTCAATTTCTCCCAGgtacattgct ... ctttgtttagGATAAATCATGGCGTGTTCGTTATATGGTCGCCAATCAGTTATATGAGCTC
EST: gi|211221964|gb|FL414368.1|FL414368
EST:     CATTGTCAATTTCTCCCAG                         GATAAATCATGGCGTGTTCGTTATATGGTCGCCAATCAGTTATATGAGCTC
genomic: CATTGTCAATTTCTCCCAGgtacattgct ... ctttgtttagGATAAATCATGGCGTGTTCGTTATATGGTCGCCAATCAGTTATATGAGCTC
EST: gi|32929909|gb|CF034721.1|CF034721
EST:     CACAAGATTGTGTAGCTCACATTCTTCCAGTCATTGTCAATTTCTCCCAG                         GATAAATCATGGCGTGTTCGTTATATGGTCGCCAATCAGTTATATGAGCTC
genomic: CACAAGATTGTGTAGCTCACATTCTTCCAGTCATTGTCAATTTCTCCCAGgtacattgct ... ctttgtttagGATAAATCATGGCGTGTTCGTTATATGGTCGCCAATCAGTTATATGAGCTC
EST: gi|32928593|gb|CF033405.1|CF033405
EST:     CACAAGATTGTGTAGCTCACATTCTTCCAGTCATTGTCAATTTCTCCCAG                         GATAAATCATGGCGTGTTCGTTATATGGTCGCCAATCAGTTATATGAGCTC
genomic: CACAAGATTGTGTAGCTCACATTCTTCCAGTCATTGTCAATTTCTCCCAGgtacattgct ... ctttgtttagGATAAATCATGGCGTGTTCGTTATATGGTCGCCAATCAGTTATATGAGCTC
EST: gi|31361222|gb|CD445579.1|CD445579
EST:     CACAAGATTGTGTAGCTCACATTCTTCCAGTCATTGTCAATTTCTCCCAG                         GATAAATCATGGCGTGTTCGTTATATGGTCGCCAATCAGTTATATGAGCTC
genomic: CACAAGATTGTGTAGCTCACATTCTTCCAGTCATTGTCAATTTCTCCCAGgtacattgct ... ctttgtttagGATAAATCATGGCGTGTTCGTTATATGGTCGCCAATCAGTTATATGAGCTC
EST: gi|13126270|gb|BG316840.1|BG316840
EST:     CACAAGATTGTGTAGCTCACATTCTTCCAGTCATTGTCAATTTCTCCCAG                         GATAAATCATGGCGTGTTCGTTATATGGTCGCCAATCAGTTATATGAGCTC
genomic: CACAAGATTGTGTAGCTCACATTCTTCCAGTCATTGTCAATTTCTCCCAGgtacattgct ... ctttgtttagGATAAATCATGGCGTGTTCGTTATATGGTCGCCAATCAGTTATATGAGCTC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cagttcagtgcattaccgctgataaatgctacttgcatatactcgctttgtttagGATAAATCATGGCGTGTTCGTTATATGGTCGCCAATCAGTTATATGAGCTCTGTGAGGCTGTTGGCCCTGAGCCCACAAG
                cgctgat  putative branch site (score: 4)
                                         ctcgcttt  putative PPT
                   tgataaat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtacattgctcccatgttggaccctatacattttgcagcaagtaatttgctttctttgtggatatattattgggagacatgtttttagttgctagaggttgataatttctcggagtcgcctcttagttttgcaacttgctgcagttcagtgcattaccgctgataaatgctacttgcatatactcgctttgtttagGATAAATCATGGCGTGTTCGTTATATGGTCGCCAATCAGTTATATGAGCTCTGTGAGGCTGTTGGCCCTGAGCCCACAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGTT