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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagtcaccccctccttttttttcttccttgggtcatagtcaggattagagctatgctgatgtgctgccttcccagGTTCAACCTTGTGTTGGTGTTTGGAGTGATAAGTGCCGTTCAAAGTATGGGAGGAGAAGACCATTTATTTTGGCTGGATGCATAATGATATGTGCTGCT

Basic information

species Zea mays
transcript GRMZM2G145107_T01
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G145107_T01 (Zea mays), 3'ss of exon 2
lower sequence: LOC_Os02g58080.1 (Oryza sativa), 3'ss of exon 2
-------------gtaagtcaccccctccttttttttc-ttccttgg---gtcatagtcaggatt--------agagctatgctgatgtgctgc----cttcccagGTTCAACCTTGTGTTGGTGTTTGGAGTGATAAGTGCCGTTCAAAGTATGGGAGGAGAAGACCATTTATTTTGGCTGGATGCATAATGATATGTGCTGCT
              ||| | |   |||| ||||||||  || | |     | |||   ||  | |        |    |||  | |||| | |     ||   ||||||||||| ||||||||||| |||||||| || ||||||||||||||||| || || ||||| || ||||||||||||||| | ||||||||   ||||
gtaagtttctgcaataattaaattcctcttttttttttgtttcataaccaggcatgtccaacactccaaacacaatagtatattaatgtcccgtgattctctgcagGTTCAACCATGTGTTGGTGTCTGGAGTGACAAATGCCGTTCAAAGTATGGAAGAAGGAGACCGTTCATTTTGGCTGGATGCTTGATGATATGCTTTGCT

upper sequence: GRMZM2G145107_T01 (Zea mays), 3'ss of exon 2
lower sequence: GLYMA18G15950.1 (Glycine max), 3'ss of exon 2
--------------------gtaagtcaccccctccttttttttcttccttgggtcatagtcaggattagagctatgctgatgtgctgc--cttccca---gGTTCAACCTTGTGTTGGTGTTTGGAGTGATAAGTGCCGTTCAAAGTATGGGAGGAGAAGACCATTTATTTTGGCTGGATGCATAATGATATGTGCTGCT
                    ||  |  ||   |   ||| |  | | |  | | |  |  |  | | ||||      |  |||||   |  |||  ||   ||||||||| || |||||| ||||||||||||| |||  ||||| || ||| || ||| ||||||| ||| |||| ||||   | |||||||||   |||
ggaatagagaattataaacagtgtgatacgtacaagtttatgctttgctcttgttggt--ttggaactagaaaatcacgtatgtgtctcaacttttcattagGTTCAACCATGCGTTGGTATTTGGAGTGATAAATGCACTTCAAGGTTTGGCAGAAGACGACCATTCATTCTGGCAGGATCTCTTATGATATGTCTGGCT

upper sequence: GRMZM2G145107_T01 (Zea mays), 3'ss of exon 2
lower sequence: Vv01s0026g01960.t01 (Vitis vinifera), 3'ss of exon 2
-------------------gtaagtcaccccctccttttttttcttccttgggtcatagtcaggattagagctatgctga----tgtgctgccttcccagGTTCAACCTTGTGTTGGTGTTTGGAGTGATAAGTGCCGTTCAAAGTATGGGAGGAGAAGACCATTTATTTTGGCTGGATGCATAATGATATGTGCTGCT
                   | |||| ||       | || || ||   |     | |  |  | |||  |  | | ||||    ||  | | |||  |||||||| |||||||||||  | |||||||| ||||||  |||||| ||||| || ||| ||||||||||| | ||||| |   ||||||| |  | ||||
ttgattttaaatctgaagtgcaagtaacaaaaatttgttattactatatatacacttcatttgaatttaaattttcctgaaaattgctcggacttttcagGTTCAGCCTTGTGTTGGGATATGGAGTGACAAGTGCTCTTCAAAATATGGAAGAAGACGACCATTTATTCTTGCTGGGTCTCTAATGATCTCAGTTGCT

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|78120050|gb|DV538434.1|DV538434
EST:     ATGCCATGGCATCATTTATTTGGCTGTGTGGGCCTATAACTGGTTTTGTG                         GTTCAACCTTGTGTTGGTGTTTGGAGTGATAAGTGCCGTTCAAAGTATGGG
genomic: ATGCCATGGCATCATTTATTTGGCTGTGTGGGCCTATAACTGGTTTTGTGgtaagtcacc ... gccttcccagGTTCAACCTTGTGTTGGTGTTTGGAGTGATAAGTGCCGTTCAAAGTATGGG
EST: gi|93282781|gb|EB675045.1|EB675045
EST:     ATGCCATGGCATCATTTATTTGGCTGTGTGGGCCTATAACTGGTTTTGTG                         GTTCAACCTTGTGTTGGTGTTTGGAGTGATAAGTGCCGTTCAAAGTATGGG
genomic: ATGCCATGGCATCATTTATTTGGCTGTGTGGGCCTATAACTGGTTTTGTGgtaagtcacc ... gccttcccagGTTCAACCTTGTGTTGGTGTTTGGAGTGATAAGTGCCGTTCAAAGTATGGG
EST: gi|93284115|gb|EB676379.1|EB676379
EST:     ATGCCATGGCATCATTTATTTGGCTGTGTGGGCCTATAACTGGTTTTGTG                         GTTCAACCTTGTGTTGGTGTTTGGAGTGATAAGTGCCGTTCAAAGTATGGG
genomic: ATGCCATGGCATCATTTATTTGGCTGTGTGGGCCTATAACTGGTTTTGTGgtaagtcacc ... gccttcccagGTTCAACCTTGTGTTGGTGTTTGGAGTGATAAGTGCCGTTCAAAGTATGGG
EST: gi|19855127|gb|BQ060179.1|BQ060179
EST:     ATGCCATGGCACCATTTATTTGGCTGTGTGGGCCTATAACTGGTTTTGTG                         GTTCAACCTTGTGTTGGTGTTTGGAGTGATAAGTGCCGTTCGAAGTATGGG
genomic: ATGCCATGGCATCATTTATTTGGCTGTGTGGGCCTATAACTGGTTTTGTGgtaagtcacc ... gccttcccagGTTCAACCTTGTGTTGGTGTTTGGAGTGATAAGTGCCGTTCAAAGTATGGG
EST: gi|78078077|gb|DV506492.1|DV506492
EST:     ATGCCATGGCATCATTTATTTGGCTGTGTGGGCCTATAACTGGTTTTGTG                         GTTCAACCTTGTGTTGGTGTTTGGAGTGATAAGTGCCGTTCAAAGTATGGG
genomic: ATGCCATGGCATCATTTATTTGGCTGTGTGGGCCTATAACTGGTTTTGTGgtaagtcacc ... gccttcccagGTTCAACCTTGTGTTGGTGTTTGGAGTGATAAGTGCCGTTCAAAGTATGGG
EST: gi|149104737|gb|EE290188.2|EE290188
EST:     ATGCCATGGCATCATTTATTTGGCTGTGTGGGCCTATAACTGGGTTTGGG                         GTTCAACCTTGTGTTGGTGT
genomic: ATGCCATGGCATCATTTATTTGGCTGTGTGGGCCTATAACTGGTTTTGTGgtaagtcacc ... gccttcccagGTTCAACCTTGTGTTGGTGT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttcttccttgggtcatagtcaggattagagctatgctgatgtgctgccttcccagGTTCAACCTTGTGTTGGTGTTTGGAGTGATAAGTGCCGTTCAAAGTATGGGAGGAGAAGACCATTTATTTTGGCTGGATGCATAATGATATGTGCTGCT
                                 tgctgat  putative branch site (score: 3)
                                           ctgccttccc  putative PPT
















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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaagtcaccccctccttttttttcttccttgggtcatagtcaggattagagctatgctgatgtgctgccttcccagGTTCAACCTTGTGTTGGTGTTTGGAGTGATAAGTGCCGTTCAAAGTATGGGAGGAGAAGACCATTTATTTTGGCTGGATGCATAATGATATGTGCTGCT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGCT