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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tgcatgtttgtatccatactgtaccacaaatggctgaaaacacttgacatgtcttagcttaccatgctggcatactaataataatgtgacttatccttagGTGTATGGTTTCTATGATGAGTGTCAGAGGAAGTATGGCAACGCCAATGCATGGCGGTATTGCACTGATGTTTTTGATTACCTTACGCTATCAGCAATCA

Basic information

species Zea mays
transcript GRMZM2G055905_T02
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G055905_T02 (Zea mays), 3'ss of exon 4
lower sequence: LOC_Os01g49690.1 (Oryza sativa), 3'ss of exon 4
tgcatgtttgtatccatactgtaccacaaatggctgaaa--acacttgacatgtcttagcttaccatgctggcatacta-ataataatgtgacttatccttagGTGTATGGTTTCTATGATGAGTGTCAGAGGAAGTATGGCAACGCCAATGCATGGCGGTATTGCACTGATGTTTTTGATTACCTTACGCTATCAGCAATCA
| || |||  |   | |     ||          |  |    ||||  |||||| || | |    ||| ||   ||  | ||| || | |    ||   |||||||||||||||||| |||||||| || ||||||||||| || || |||||||||||||||||||| ||||||||||| |||||||| || ||||||||||
taca-gttcatcctcctgacagactttgtgctcatatatctgcactacacatgtatttggtgcttatgatgcagtaacacatagtatttt--tctaattttagGTGTATGGTTTCTACGATGAGTGCCAAAGGAAGTATGGGAATGCGAATGCATGGCGGTATTGCACCGATGTTTTTGACTACCTTACTCTTTCAGCAATCA

upper sequence: GRMZM2G055905_T02 (Zea mays), 3'ss of exon 4
lower sequence: GLYMA10G43470.1 (Glycine max), 3'ss of exon 4
tgcatg-tttgtatccatactgtaccacaaatggctgaaaacacttgacatgtcttagcttaccatgctggcatactaataataatgtgacttatcctt-----agGTGTATGGTTTCTATGATGAGTGTCAGAGGAAGTATGGCAACGCCAATGCATGGCGGTATTGCACTGATGTTTTTGATTACCTTACGCTATCAGCAATCA
   ||  ||  ||       | |            |   || ||| || ||| |  ||  || ||| |||   || |  ||||  ||| | |||   ||     |||| ||||| || |||||||| || ||||||||||||||||| |||||||| ||||||||||| || ||||| ||||| ||||| || || || ||||| |
---ataattcataatggagatatgaattgtggtaatactaaaactagaaatgcccaag--tatcatactgattta-tgttaattttgtaatttactgttttgctagGTCTATGGATTTTATGATGAATGCCAGAGGAAGTATGGCAATGCCAATGCTTGGCGGTATTGTACAGATGTGTTTGACTACCTAACTCTTTCTGCAATTA

upper sequence: GRMZM2G055905_T02 (Zea mays), 3'ss of exon 4
lower sequence: GLYMA0048S00290.2 (Glycine max), 3'ss of exon 4
-tgcatgtttgtatccat-actgtaccacaaatggctgaaaacacttgacatgtcttagcttaccatgctggcatactaataataatgtgacttatccttagGTGTATGGTTTCTATGATGAGTGTCAGAGGAAGTATGGCAACGCCAATGCATGGCGGTATTGCACTGATGTTTTTGATTACCTTACGCTATCAGCAATCA
    | | |  ||    | |  || ||  | || |   |  | |  ||     |  |||  | |||   |    || || |  |||| | |  | |   ||||| ||||| || |||||||| || |||||||||||||| || || ||||| ||||| ||||| || ||||||||||| || ||||| || || ||||| |
agataaggtattaattgtgaaagtgcctaagattggaaattataaatgttgaattctagtatgccactttatgttaata-ttgtaatat-atgtttttctagGTCTATGGATTTTATGATGAATGCCAGAGGAAGTATGGGAATGCTAATGCTTGGCGATATTGTACAGATGTTTTTGACTATCTTACTCTTTCTGCAATTA

upper sequence: GRMZM2G055905_T02 (Zea mays), 3'ss of exon 4
lower sequence: GLYMA20G23310.4 (Glycine max), 3'ss of exon 4
tgcatgtttgtatccatactgtac-cacaaatggctgaaa-----acacttgacatgtcttagcttaccatgctggcatactaataataatgtgacttatcctt-----agGTGTATGGTTTCTATGATGAGTGTCAGAGGAAGTATGGCAACGCCAATGCATGGCGGTATTGCACTGATGTTTTTGATTACCTTACGCTATCAGCAATCA
         |  | |||| || |   |  ||| |  ||||     | ||  || ||| |  ||  || |||| ||   || |  ||||  ||| | |||   ||     |||| ||||| || |||||||| || ||||||||||||||||| |||||||| ||||||||||| || ||||| ||||| ||  | || || || ||||| |
--------agatttcataatggagatatgaattgtggaaatactaaaaccagaaatgccaaag--tatcatgatgattta-tgttaattttgtaatttactgttttgctagGTCTATGGATTTTATGATGAATGCCAGAGGAAGTATGGCAATGCCAATGCTTGGCGGTATTGTACAGATGTGTTTGACTATTTAACACTTTCTGCAATTA

upper sequence: GRMZM2G055905_T02 (Zea mays), 3'ss of exon 4
lower sequence: GLYMA10G43480.1 (Glycine max), 3'ss of exon 4
-tgcatgtttgtatccatactgtaccacaaatggctgaaaacacttgacatgtcttagcttaccatgctggcatactaataataatgtgacttatcctt-----agGTGTATGGTTTCTATGATGAGTGTCAGAGGAAGTATGGCAACGCCAATGCATGGCGGTATTGCACTGATGTTTTTGATTACCTTACGCTATCAGCAATCA
 | ||    |      ||| |        ||   || ||| ||   || |||    ||  || |||||||   || |  |||| |||| | |||   ||     |||| ||||| || |||||||| || ||||||||||||||||| |||||||| ||||| ||||| || ||||| ||||| || || || || || ||||| |
attcaaaagtaaggtaatattaattgtggaaatactaaaacca---gaaatgcaaaag--tatcatgctgattta-tgttaattatgtaatttactgttttgctagGTCTATGGATTTTATGATGAATGCCAGAGGAAGTATGGCAATGCCAATGCTTGGCGCTATTGTACAGATGTGTTTGACTATCTAACACTTTCTGCAATTA

upper sequence: GRMZM2G055905_T02 (Zea mays), 3'ss of exon 4
lower sequence: AT3G19980.1 (Arabidopsis thaliana), 3'ss of exon 4
-tgcatgtttgtatccatactgtaccacaaatggctgaaaacacttgacatgtcttagcttaccatgctggcatacta-ataataatgtgactta--tccttagGTGTATGGTTTCTATGATGAGTGTCAGAGGAAGTATGGCAACGCCAATGCATGGCGGTATTGCACTGATGTTTTTGATTACCTTACGCTATCAGCAATCA
 ||||| || ||     | ||| || |   |||    |||  |         |||   | |   |  |    |||  | | ||  || ||| |||  |  ||||||||||||||||||||| || || |||||||||||||| ||||| ||||| ||||| |||||||| ||||||||||| || ||||| || ||||| || |
atgcat-ttcgtgaatctgctg-acta--gatgatcaaaattatacatggattctcgacattgaactcctttataacacagaaccatttgatttacttttttagGTGTATGGTTTCTATGACGAATGCCAGAGGAAGTATGGTAACGCTAATGCGTGGCGATATTGCACAGATGTTTTTGACTATCTTACCCTGTCAGCTATTA

upper sequence: GRMZM2G055905_T02 (Zea mays), 3'ss of exon 4
lower sequence: AT1G50370.1 (Arabidopsis thaliana), 3'ss of exon 4
tgcatgtttgtatccatactgtaccacaaatggctgaaaacacttgacatgtctta---gcttaccatgctggcatactaataataatgtgac----ttatcctt---agGTGTATGGTTTCTATGATGAGTGTCAGAGGAAGTATGGCAACGCCAATGCATGGCGGTATTGCACTGATGTTTTTGATTACCTTACGCTATCAGCAATCA
           |||||   |  |  || || |  || |   |  |    || | |    | | |   |  | |  | || | | |   ||  |    ||||  ||   ||||||||||||||||||| || || || ||||||||||| || || ||||| ||| | |||||||| ||||||||||| || ||||| || ||||| || |
---------acatccactgtcaaggacgaa-gattgtagtgatattttgtgccctgcaggttcatttttatagttttcttaaattgtcgtaccaattttatatttgctagGTGTATGGTTTCTATGACGAATGCCAAAGGAAGTATGGTAATGCTAATGCTTGGAGATATTGCACGGATGTTTTTGACTATCTTACACTTTCAGCTATTA

upper sequence: GRMZM2G055905_T02 (Zea mays), 3'ss of exon 4
lower sequence: Vv10s0071g00950.t01 (Vitis vinifera), 3'ss of exon 4
tgcatgtttgtatccatactgtaccacaaatggctgaa----aacacttgacatgtcttagcttaccatgctggcatactaata-ataatgtgacttatccttagGTGTATGGTTTCTATGATGAGTGTCAGAGGAAGTATGGCAACGCCAATGCATGGCGGTATTGCACTGATGTTTTTGATTACCTTACGCTATCAGCAATCA
    |||||     ||||   |   ||| || ||  ||     |||   ||  |  |     |||  ||  |    || || |  ||| | |   |  |    |||| |||||||||||||||||||| ||||||||||| || || || |||||||||||||| ||||| ||||||||||| ||||| || || || || || |
-aactgtttccccacataggatgaaacacattgcacaactgtgacaagagatttaccaatatttaggatatt----tattagtgtatacttttcttcttttccagGTCTATGGTTTCTATGATGAGTGCCAGAGGAAGTACGGAAATGCTAATGCATGGCGGTACTGCACAGATGTTTTTGACTACCTAACCCTCTCTGCGATAA

upper sequence: GRMZM2G055905_T02 (Zea mays), 3'ss of exon 4
lower sequence: PP1S31_220V6.1 (Physcomitrella patens), 3'ss of exon 4
tgcatgtttgtatccatactgtaccacaaatggctgaaaacacttgacatgtcttagctta-ccatgctggcat--actaataataatgtgacttatcct-tagGTGTATGGTTTCTATGATGAGTGTCAGAGGAAGTATGGCAACGCCAATGCATGGCGGTATTGCACTGATGTTTTTGATTACCTTACGCTATCAGCAATCA
    || || | || |   |  | |  |  ||  ||    ||     ||  | || |  || ||  |  |      | |       | |||   |  |    |||| ||||| || |||||||| |||||| | |||||||| ||| | ||||| ||||||||||||||||| |||||||| ||||| || || || || ||||
---ctgattttctctaagatacagc-tatctgtgtgcgtgcatccatcaatttttggaataaccgagacgtttctgattttgtccgaagtggtatgcctgacagGTCTATGGATTTTATGATGAATGTCAGCGTAAGTATGGAAACCCAAATGCTTGGCGGTATTGCACTGACGTTTTTGACTACCTGACACTCTCGGCTATCA

upper sequence: GRMZM2G055905_T02 (Zea mays), 3'ss of exon 4
lower sequence: PP1S207_36V6.1 (Physcomitrella patens), 3'ss of exon 4
tgc-atgtttgtatccatactgtaccacaaatggctgaaaacacttgacatgtcttagcttaccatgctggcatactaataataatgtgacttatcct-tagGTGTATGGTTTCTATGATGAGTGTCAGAGGAAGTATGGCAACGCCAATGCATGGCGGTATTGCACTGATGTTTTTGATTACCTTACGCTATCAGCAATCA
||| || | | ||| |||  || |    |  ||  |  ||  ||||    |||   | | |   ||| ||      |   |   |  ||   | |     |||| ||||| || ||||| || || ||| |||||||||| ||| | ||||| |||||||| ||||||||||||||||| |||||||| || ||||| || |
tgccatatatttatgcatg-tgaaagttatctgaattcaattactttttgtgtgg-accatgaaatgttgttggttttgaacggaattggtgtgtttgacagGTATATGGATTTTATGACGAATGCCAGCGGAAGTATGGAAACCCAAATGCTTGGCGGTACTGCACTGATGTTTTTGACTACCTTACACTCTCAGCCATAA

upper sequence: GRMZM2G055905_T02 (Zea mays), 3'ss of exon 4
lower sequence: EFJ05314 (Selaginella moellendorffii), 3'ss of exon 4
tgcatgtttgtatccatactgtaccacaaatggctgaaaacacttgacatgtcttagcttaccatgctggcatactaata-ataatgtgacttatccttagGTGTATGGTTTCTATGATGAGTGTCAGAGGAAGTATGGCAACGCCAATGCATGGCGGTATTGCACTGATGTTTTTGATTACCTTACGCTATCAGCAATCA
        ||  ||   | | |   | |||       ||||  |||   |  |  | |  |      |  | | ||||    |  | |||         |||||||||||||||||||||| ||  || |||||||||| ||  | || || ||||| || |||||||| ||||| ||||| || ||  | || || ||||
-------gtgattctcgatttttttaaaaa-------aaacttttgttct-ccccaacgaaaagaattatctttctaacgcgttgtttga---gcttccagGTGTATGGTTTCTATGATGAATGCGAGCGGAAGTATGGAAATCCAAACGCTTGGCGTTACTGCACTGACGTTTTCGATTATCTAACTATCTCTGCGATCA

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|5871474|gb|AW017945.1|AW017945
EST:     CACACATAACCCTTCTGCGTGGAAATCATGAAAGTAGGCAGTTGACACAG                         GTGTATGGTTTCTATGATGAGTGTCAGAGGAAGTATGGCAACGCCAATGCA
genomic: CACACATAACCCTTCTGCGTGGAAATCATGAAAGTAGGCAGTTGACACAGgtatattctt ... ttatccttagGTGTATGGTTTCTATGATGAGTGTCAGAGGAAGTATGGCAACGCCAATGCA
EST: gi|38568907|gb|CF974792.1|CF974792
EST:     CACACATAACCCTTCTGCGTGGAAATCATGAAAGTAGGCAGTTGGCACAG                         GTGTATGGTTTCTATGATGAGTGTCAGAGGAAGTATGGCAACGCCAATGCA
genomic: CACACATAACCCTTCTGCGTGGAAATCATGAAAGTAGGCAGTTGACACAGgtatattctt ... ttatccttagGTGTATGGTTTCTATGATGAGTGTCAGAGGAAGTATGGCAACGCCAATGCA
EST: gi|32856737|gb|CD996418.1|CD996418
EST:     CACACATAACCCTTCTGCGTGGAAATCATGAAAGTAGGCAGTTGACACAG                         GTGTATGGTTTCTATGATGAGTGTCAGAGGAAGTATGGCAACGCCAATGCA
genomic: CACACATAACCCTTCTGCGTGGAAATCATGAAAGTAGGCAGTTGACACAGgtatattctt ... ttatccttagGTGTATGGTTTCTATGATGAGTGTCAGAGGAAGTATGGCAACGCCAATGCA
EST: gi|211170203|gb|FL095738.1|FL095738
EST:     CACACATAACCCTTCTGCGTGGAAATCATGAAAGTAGGCAGTTGACACAG                         GTGTATGGTTTCTATGATGAGTGTCAGAGGAAGTATGGCAACGCCAATGCA
genomic: CACACATAACCCTTCTGCGTGGAAATCATGAAAGTAGGCAGTTGACACAGgtatattctt ... ttatccttagGTGTATGGTTTCTATGATGAGTGTCAGAGGAAGTATGGCAACGCCAATGCA
EST: gi|32826793|gb|CD966471.1|CD966471
EST:     CACACATAACCCTTCTGCGTGGAAATCATGAAAGTAGGCAGTTGACACAG                         GTGTATGGTTTCTATGATGAGTGTCAGAGGAAGTATGGCAACGCCAATGCA
genomic: CACACATAACCCTTCTGCGTGGAAATCATGAAAGTAGGCAGTTGACACAGgtatattctt ... ttatccttagGTGTATGGTTTCTATGATGAGTGTCAGAGGAAGTATGGCAACGCCAATGCA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gacatgtcttagcttaccatgctggcatactaataataatgtgacttatccttagGTGTATGGTTTCTATGATGAGTGTCAGAGGAAGTATGGCAACGCCAATGCATGGCGGTATTGCACTGATGTTTTTGATTACCTTACGCTATCAGCAATCA
                           tactaat  putative branch site (score: 1)
                                            cttatcctt  putative PPT
                          atactaataataatgt  TA-rich tract