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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgagccctccgccggcctctagcgccaccttgttctccatccacatctcgcgcctccgcgcttcaccccatttcctagtgtttgtgacggctggccggtgcaggccgcgaccgcgccctcccggcctagggtttcgatctcgcgccgattcatctgctacctcgcggtttgactctgctcttgcttgacgagtgcagGAGGGCGACAGTACCAACCTCGACGCGGCTATAGAGTCGCTCCTGAACGTGGAGAAGCAGATGAGGCTGGCCGGCGATGTCGCCGGCACGCGGAAGGCCG

Basic information

species Zea mays
transcript GRMZM2G013750_T03
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G013750_T03 (Zea mays), 3'ss of exon 1
lower sequence: LOC_Os03g63430.2 (Oryza sativa), 3'ss of exon 1
gtgagccctccgccggcctctagcgccaccttgttctccatccacatctcgcgcctccgcgcttcaccccatttcctagtgtttgtgacggctggccggtgcaggccgcgaccgcgccctcccggcctagggtttcgatctcgcgccgattcatctgctacctcgcggtttgactctgctcttgcttgacgagtgcagGAGGGCGACAGTACCAACCTCGACGCGGCTATAGAGTCGCTCCTGAACGTGGAGAAGCAGATGAGGCTGGCCGGCGATGTCGCCGGCACGCGGAAGGCCG
                      | |    |   | |  | ||| | || | | || |  | || | |||   |  |  | ||||  | |  |  ||| |  | | ||||| || ||| || |    ||||||||||||||||  || | || ||||| | ||| ||  | |||| ||| |  |  | |||   ||||||||||  |||||||||||||||| ||||| |||||||||||||| ||||||||||||||||||||||||||||||||||||||||||||| |||||||||
----------------------gtgagctcacctccctcctcccc-tcccccaccccgaccctccgcccgcctctccggggttttggccttcccgcccgccccg-ccgcggcc-cgcacttctcatctagggtttcgatctcttgcgggttgatctgatgccttgcaatctgaccctgtttcttgtggaccgatgcagGAGGGTAACAGTACCAACCTCGATGCGGCGATAGAGTCGCTCCTCAACGTGGAGAAGCAGATGAGGCTGGCCGGCGATGTCGCCGGCACGAGGAAGGCCG

upper sequence: GRMZM2G013750_T03 (Zea mays), 3'ss of exon 1
lower sequence: GLYMA05G32030.2 (Glycine max), 3'ss of exon 1
gtgagccctccgccggcctctagcgccaccttgttctccatccacatctcgcgcctccgcgcttcaccccatttcctagtgtttgtgacggctggccggtgcaggccgcgaccgcgccctcccggcctagggtttcgatctcgcgccgatt-catctgctacctcgcggtttgactctgctcttgcttgacgagtgcagGAGGGCGACAGTACCAACCTCGACGCGGCTATAGAGTCGCTCCTGAACGTGGAGAAGCAGATGAGGCTGGCCGGCGATGTCGCCGGCACGCGGAAGGCCG---
                                                                                   |   ||| ||  |  | |  |      |        | | |  ||    ||      | | |   | |  | |||    |||      ||| | |  | ||  | | | | | | |||             ||  | |||||||| ||||||    | |||||||||||||||||||||||||| ||||| || || || || ||  | ||||| |   
---------------------------------------------------------------------------------ccttcaacgact--ctagggttgttt---attttttttttctgaactgaaattcgatgattgtggtcactgtaactgacggctccta---tgaattttttatttgtagGCAAATACGGGA-------------AATTTAGACGCGGCGATAGAGCAATTGCTGAACGTGGAGAAGCAGATGAGGCTCGCCGGTGACGTGGCAGGTACCAGAAAGGCGGCTA

upper sequence: GRMZM2G013750_T03 (Zea mays), 3'ss of exon 1
lower sequence: GLYMA08G15340.1 (Glycine max), 3'ss of exon 1
gtgagccctccgccggcctctagcgccaccttgttctccatccacatctcgcgcctccgcgcttcaccccatttcctagtgtttgtgacggctggccggtgcaggccgcgaccgcgccctcccggcctagggtttcgatctcgcgccgattcatctgctacctcgcggtttgactctgctcttgcttgacgagtgcagGAGGGCGA-CAGTACCAACCTCGACGCGGCTATAGAGTCGCTCCTGAACGTGGAGAAGCAGATGAGGCTGGCCGGCGATGTCGCCGGCACGCGGAAGGCCG---
                                                                                                       |||  | ||  | |       |  ||   ||| | ||| |  | ||    ||  | |    |     |||   ||   || | ||   | |    |  |||||  |     ||  | |||||||| ||||||    | |||||||||||||||||||||||||| ||||| || || || || ||  | || || |   
----------------------------------------------------------------------------------------------------tttggcttcaacgactctggggttgtttatttttttgttct-gaactgaaat-tcgacgattgtggtaactgaaattgacgtttcctgtgaattttttgtagGCGAATACGGGGAATTTAGACGCGGCGATAGAGCAATTGCTGAACGTGGAGAAGCAGATGAGGCTCGCCGGTGACGTGGCGGGTACCAGAAAAGCAGCCA

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|211149905|gb|FL367833.1|FL367833
EST:     TCGTCGTCGCCTCGCCGTCTCCTCCGCCGTTGCCTGCGATCCCGATCATG                         GAGGGCGACAGTACCAACCTCGACGCGGCTATAGAGTCGCTCCTGARSGTG
genomic: TCGTCGTCGCCTCGCTGTCTCCTCCGCCGTTGCCTGCGATCCCGATCATGgtgagccctc ... acgagtgcagGAGGGCGACAGTACCAACCTCGACGCGGCTATAGAGTCGCTCCTGAACGTG
EST: gi|13557648|gb|BG549004.1|BG549004
EST:     GTCTCCTCCGCCGTGTGCCTGCGATCCCGATCATG                         GAGGGCGACAGTACCAACCTCGACGCGGCTATAGAGTCGCTCCTGAACGTG
genomic: GTCTCCTCCGCCGT-TGCCTGCGATCCCGATCATGgtgagccctc ... acgagtgcagGAGGGCGACAGTACCAACCTCGACGCGGCTATAGAGTCGCTCCTGAACGTG
EST: gi|13316089|gb|BG410536.1|BG410536
EST:     TGCGATCCCGATCATG                         GAGGGCGACAGTACCAACCTCGACGCGGCTATAGAGTCGCTCCTGAACGTG
genomic: TGCGATCCCGATCATGgtgagccctc ... acgagtgcagGAGGGCGACAGTACCAACCTCGACGCGGCTATAGAGTCGCTCCTGAACGTG
EST: gi|31909275|gb|CD650837.1|CD650837
EST:     TCGTCGTCGCCTCGCTGTCTCCTCCGCCGTTGCCTGCGATCCCGATCATG                         GAGGGCGACAGTACCAACCTCGACGCGGCTATAGAGTCGCTCCTGAACGTG
genomic: TCGTCGTCGCCTCGCTGTCTCCTCCGCCGTTGCCTGCGATCCCGATCATGgtgagccctc ... acgagtgcagGAGGGCGACAGTACCAACCTCGACGCGGCTATAGAGTCGCTCCTGAACGTG
EST: gi|13316088|gb|BG410535.1|BG410535
EST:     TCGTCGTCGCCTCGCTGTCTCCTCCGCCGTTGCCTGCGATCCCGATCATG                         GAGGGCGACAGTACCAACCTCGACGCGGCTATAGAGTCGCTCCTGAACGTG
genomic: TCGTCGTCGCCTCGCTGTCTCCTCCGCCGTTGCCTGCGATCCCGATCATGgtgagccctc ... acgagtgcagGAGGGCGACAGTACCAACCTCGACGCGGCTATAGAGTCGCTCCTGAACGTG
EST: gi|4753426|gb|AI657336.1|AI657336
EST:     CTCCTCCGCCGTTGCCTGCGATCCCGATCATG                         GAGGGCGACAGTACCAACCTCGACGCGGCTATAGAGTCGCTCCTGAACGTG
genomic: CTCCTCCGCCGTTGCCTGCGATCCCGATCATGgtgagccctc ... acgagtgcagGAGGGCGACAGTACCAACCTCGACGCGGCTATAGAGTCGCTCCTGAACGTG
EST: gi|211157243|gb|FL334276.1|FL334276
EST:     TCGTCGTCGCCTCGCCGTCTCCTCCGCCGTTGCCTGCGATCCCGATCATG                         GAGGGCGACAGTACCAACCTCGACGCGGCTATAGAGTCGCTCCTGAACGTG
genomic: TCGTCGTCGCCTCGCTGTCTCCTCCGCCGTTGCCTGCGATCCCGATCATGgtgagccctc ... acgagtgcagGAGGGCGACAGTACCAACCTCGACGCGGCTATAGAGTCGCTCCTGAACGTG
EST: gi|9952312|gb|BE638895.1|BE638895
EST:     GCCTCGCTGTCTCCTCCGCCGTTGCCTGCGATCCCGATCATG                         GAGGGCGACAGTACCAACCTCGACGCGGCTATAGAGTCGCGTCCTGAACGT
genomic: GCCTCGCTGTCTCCTCCGCCGTTGCCTGCGATCCCGATCATGgtgagccctc ... acgagtgcagGAGGGCGACAGTACCAACCTCGACGCGGCTATAGAGTCGC-TCCTGAACGT
EST: gi|211187929|gb|FL314081.1|FL314081
EST:     TCGTCGTCGCCTCGCCGTCTCCTCCGCCGTTGCCTGCGATCCCGATCATG                         GAGGGCGACAGTACCAACCTCGACGCGGCTATAGAGTCGCTCCTGAACGTG
genomic: TCGTCGTCGCCTCGCTGTCTCCTCCGCCGTTGCCTGCGATCCCGATCATGgtgagccctc ... acgagtgcagGAGGGCGACAGTACCAACCTCGACGCGGCTATAGAGTCGCTCCTGAACGTG
EST: gi|148974705|gb|EE025514.2|EE025514
EST:     GCTGTCTCCTCCGCCGTTGCCTGCGATCCCGATCATG                         GAGGGCGACAGTACCAACCTCGACGCGGCTATAGAGTCGCTCCTGAACGTG
genomic: GCTGTCTCCTCCGCCGTTGCCTGCGATCCCGATCATGgtgagccctc ... acgagtgcagGAGGGCGACAGTACCAACCTCGACGCGGCTATAGAGTCGCTCCTGAACGTG
EST: gi|211448768|gb|FL325252.1|FL325252
EST:     TCGTCGTCGCCTCGCCGTCTCCTCCGCCGTTGCCTGCGATCCCGATCATG                         GAGGGCGACAGTACCAACCTCGACGCGGCTATAGAGTCGCTCCTGAACGTG
genomic: TCGTCGTCGCCTCGCTGTCTCCTCCGCCGTTGCCTGCGATCCCGATCATGgtgagccctc ... acgagtgcagGAGGGCGACAGTACCAACCTCGACGCGGCTATAGAGTCGCTCCTGAACGTG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cgccgattcatctgctacctcgcggtttgactctgctcttgcttgacgagtgcagGAGGGCGACAGTACCAACCTCGACGCGGCTATAGAGTCGCTCCTGAACGTGGAGAAGCAGATGAGGCTGGCCGGCGATGTCGCCGGCACGCGGAAGGCCG
                                        gcttgac  putative branch site (score: 4)
















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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgagccctccgccggcctctagcgccaccttgttctccatccacatctcgcgcctccgcgcttcaccccatttcctagtgtttgtgacggctggccggtgcaggccgcgaccgcgccctcccggcctagggtttcgatctcgcgccgattcatctgctacctcgcggtttgactctgctcttgcttgacgagtgcagGAGGGCGACAGTACCAACCTCGACGCGGCTATAGAGTCGCTCCTGAACGTGGAGAAGCAGATGAGGCTGGCCGGCGATGTCGCCGGCACGCGGAAGGCCG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CAGATG