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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaatgcaacatatctatttgattgtacttatacctttgtctgttttgatggtagcatgaatgtctagaaatatctgcgaattctaaatgcctgttgagagaataatttgggatatgacaaatgtgattgtattaatacctttcagGCCAAGACCACCAAGAAGATTGTTCTGAAGCTGCAGTGCCAGAGCTGCAAGCACTACTCACAGCACGCCATCAAG

Basic information

species Zea mays
transcript GRMZM2G103059_T02
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G103059_T01 (Zea mays), 3'ss of exon 2
lower sequence: LOC_Os07g33915.1 (Oryza sativa), 3'ss of exon 1
gtaatgcaacatatctatttgattgtacttatacctttgtctgttttgatggtagcatgaatgtctagaaatatctgcgaattctaaatgcctgttgagagaataatttgggatatgacaaatgtgattgtattaatacctttcagGCCAAGACCACCAAGAAGATTGTTCTGAAGCTGCAGTGCCAGAGCTGCAAGCACTACTCACAGCACGCCATCAAG
                                  |    || |       |    |   | |||          | || |  || ||| ||     | | | ||  ||   | ||||| | ||| | |  | ||       ||||||| || ||||||||||||||||| ||||||||||| ||||| ||||||||||| ||||| |||||| ||||||||
---------------------------------gccccatc-gcgccaccgcgcacggcattgttgctctcctccggccaggtccaaaagca----gggtgcatttttcatgttatgatacatg-gttcctgtt-------ttcagGCAAAAACCACCAAGAAGATTGTGCTGAAGCTGCAATGCCAAAGCTGCAAGCATTACTCCCAGCACCCCATCAAG

upper sequence: GRMZM2G103059_T01 (Zea mays), 3'ss of exon 2
lower sequence: LOC_Os07g33860.1 (Oryza sativa), 3'ss of exon 2
gtaatgcaacatatctatttgattgtacttatacctttgtctgttttgatggtagcatgaatgtctagaaatatctgcgaattctaaatgcctgttgagagaataatttgggatatgacaaatgtgattgtat-taatacct---ttcagGCCAAGACCACCAAGAAGATTGTTCTGAAGCTGCAGTGCCAGAGCTGCAAGCACTACTCACAGCACGCCATCAAG
                                            ||  |||  | ||||  ||   | ||  |||    | || |||| |  | |   ||   | |  || |  ||     |||| ||  ||  |  | |||   ||||||| || ||||||||||||||||| ||||||||||| ||||| ||||||||||| ||||| |||||| ||||||||
-------------------------------------------gttcaatgcaaacatg--tggtaataaccatcacgtagttttaaa-gtatat---gactttcagctgtg-catttttcatgttatgatacatggttcctgttttcagGCAAAAACCACCAAGAAGATTGTGCTGAAGCTGCAATGCCAAAGCTGCAAGCATTACTCCCAGCACCCCATCAAG

upper sequence: GRMZM2G103059_T01 (Zea mays), 3'ss of exon 2
lower sequence: LOC_Os07g33898.1 (Oryza sativa), 3'ss of exon 2
----------------------gtaatgcaacatatctatttgattgtacttatacctttgtctgttttgatggtagcatgaatgtctag-------aaatatctgcgaat--tctaaatgcctgttgagagaat---aatttgggatatga----caaatgtgattgtat-taatacct---ttcagGCCAAGACCACCAAGAAGATTGTTCTGAAGCTGCAGTGCCAGAGCTGCAAGCACTACTCACAGCACGCCATCAAG
                       | | |||     | | | |||||||   | | | || |     | || ||  |  ||   |||||         ||| || ||  |||   |   |||    || |  | ||   | |||  | | ||        |||| ||  ||  |  | |||   ||||||| || ||||||||||||||||| ||||||||||| ||||| ||||||||||| ||||| |||||| ||||||||
gtattgtgacagtttatatgtgattacgcagtgc-tgtgtgtgattgtctctcttcattagaaacatatggtgtcatgatttgtgtctgttcaatgcaaacatgtggcaataaccatcatgtagttttaatgtatctgactttcagctgtgcatttttcatgttatgatacatggttcctgttttcagGCAAAAACCACCAAGAAGATTGTGCTGAAGCTGCAATGCCAAAGCTGCAAGCATTACTCCCAGCACCCCATCAAG

upper sequence: GRMZM2G103059_T01 (Zea mays), 3'ss of exon 2
lower sequence: LOC_Os07g33880.1 (Oryza sativa), 3'ss of exon 2
--------------------------------gtaatgcaacatatctatttgattgtacttatacctt----tgtctgttttgatggtagcatgaatgtctagaa-atatctgcgaattctaaatgcctg---ttgagagaata---atttgggatatga----caaatgtgattgtat-taatacc---tttcagGCCAAGACCACCAAGAAGATTGTTCTGAAGCTGCAGTGCCAGAGCTGCAAGCACTACTCACAGCACGCCATCAAG
                                ||  ||    |       || |||  |    |||  |    ||  || | |    ||   |||  | | || ||   || ||  |||    |   | |    || |  | ||     |||  | | ||        |||| ||  ||  |  | ||   |||||||| || |||||||||||||| || ||||||||||| ||||| ||||||||||| ||||| |||||| ||||||||
gtactgtgacagtttatatatgattatgcagtgttgtgtgtgactctctgttcattagaaacgtacggtgtcatgattgatgtagcagtgatatgtgtctgtacaatgcatgtggcaataaccatcacgtagttttaattgcatgtggctttcagctgtgcatttttcatgttatgatacatggttcctgttttcagGCAAAAACCACCAAGAAGATCGTGCTGAAGCTGCAATGCCAAAGCTGCAAGCATTACTCCCAGCACCCCATCAAG

upper sequence: GRMZM2G103059_T01 (Zea mays), 3'ss of exon 2
lower sequence: GLYMA15G05670.2 (Glycine max), 3'ss of exon 2
gtaatgcaacatatctatttgattgtacttatacctttgtctgttttgatggtagcatgaatgtctagaaatatctgcgaattctaaatgcctgttgagagaataatttgggatatgacaaatgtgattgtattaatacctttcagGCCAAGACCACCAAGAAGATTGTTCTGAAGCTGCAGTGCCAGAGCTGCAAGCACTACTCACAGCACGCCATCAAG----
                                            || | ||||   ||   |   || || |   |  |||||    ||   | ||          |||  | |   | |||| |  || |||| | |      |||| || |||||||||||||||||||||| | |||| |||||| | ||||||||   ||| || ||||| || |||    
-------------------------------------------gttcgttggttaaatatttcgttataagtgcataggaatta-ggatctttttt----------tttttgctgacaaaaatatatttttatttaaaat----agGCTAAAACCACCAAGAAGATTGTTCTGAGGTTGCAATGCCAGGGTTGCAAGCATGTCTCCCAACACGCTATTAAGGTTA

upper sequence: GRMZM2G103059_T01 (Zea mays), 3'ss of exon 2
lower sequence: GLYMA08G19320.1 (Glycine max), 3'ss of exon 2
gtaatgcaacatatctatttgattgtacttatacctttgtctgttttgatggtagcatgaatgtctagaaatatctgcgaattctaaatgcctgttgagagaataatttgggatatgacaaatgtgattgtattaatacctt-tcagGCCAAGACCACCAAGAAGATTGTTCTGAAGCTGCAGTGCCAGAGCTGCAAGCACTACTCACAGCACGCCATCAAG
                                                                   | ||  |||    |  |||| ||| |   ||   |  | |||      |||||||     || ||||  ||  |  | |||| ||||||||||||||||||||||||| | |||| |||||| | ||||||||   ||| || ||||| || |||
-------------------------------------------------------------------gtaacctctcgttaacctaagtgcatag-gaattaggagtttttttcctgacaaaaacatttttatttttaattgattagGCTAAGACCACCAAGAAGATTGTTCTGAGGTTGCAATGCCAGGGTTGCAAGCATGTCTCCCAACACGCTATTAAG

upper sequence: GRMZM2G103059_T01 (Zea mays), 3'ss of exon 2
lower sequence: GLYMA15G05670.1 (Glycine max), 3'ss of exon 2
gtaatgcaacatatctatttgattgtacttatacctttgtctgttttgatggtagcatgaatgtctagaaatatctgcgaattctaaatgcctgttgagagaataatttgggatatgacaaatgtgattgtattaatacctttcagGCCAAGACCACCAAGAAGATTGTTCTGAAGCTGCAGTGCCAGAGCTGCAAGCACTACTCACAGCACGCCATCAAG
                                            || | ||||   ||   |   || || |   |  |||||    ||   | ||          |||  | |   | |||| |  || |||| | |      |||| || |||||||||||||||||||||| | |||| |||||| | ||||||||   ||| || ||||| || |||
-------------------------------------------gttcgttggttaaatatttcgttataagtgcataggaatta-ggatctttttt----------tttttgctgacaaaaatatatttttatttaaaat----agGCTAAAACCACCAAGAAGATTGTTCTGAGGTTGCAATGCCAGGGTTGCAAGCATGTCTCCCAACACGCTATTAAG

upper sequence: GRMZM2G103059_T01 (Zea mays), 3'ss of exon 2
lower sequence: AT3G23390.1 (Arabidopsis thaliana), 3'ss of exon 2
gtaatgcaacatatc-tat-ttgattgtacttataccttt------gtctgttttgatggtagcatgaatgtcta--gaaatatctgc----gaattctaaatgcctgttgagag--------------aataatttgggatatg-acaaatgtg-attgtattaataccttt--cagGCCAAGACCACCAAGAAGATTGTTCTGAAGCTGCAGTGCCAGAGCTGCAAGCACTACTCACAGCACGCCATCAAG
||||       |||| |   ||||||||  ||  |  ||       ||||  || | ||  |  | | |  | ||  |||  || |      ||||| |  | |   | || |||              |||| | |  | | || ||  |  |  ||  | | |||    ||  ||||| |||||||| |||||||||||| ||| ||| ||||| || |||||||||||||  || ||||   | ||||||
gtaacattgattatcatgcattgattgttttttcagtttgaattaggtctagttagttgaaatgaggtagttttaaggaaccatttatagtagaattttggaagtgagctgtgaggaaacagacattccaatagtctcagttttggactgagatacatcttgtgaatcttgttaacagGCTAAGACCACGAAGAAGATTGTTTTGAGGCTTCAGTGTCAAAGCTGCAAGCACTTTTCGCAGCGTCCTATCAAG

upper sequence: GRMZM2G103059_T01 (Zea mays), 3'ss of exon 2
lower sequence: Vv13s0064g00880.t01 (Vitis vinifera), 3'ss of exon 2
gtaatgcaacatatctatttgattgtacttatacctttgtctgttttgatggtagcatgaatgtctagaaatatctgcgaattctaaatgcctgttgagagaat--aatttgggatatgacaaat--gtgattgtattaataccttt-cagGCCAAGACCACCAAGAAGATTGTTCTGAAGCTGCAGTGCCAGAGCTGCAAGCACTACTCACAGCACGCCATCAAG
                                                  |||    || ||   ||||| | |  ||    || || |  || |  ||  |||  |   |      | | | ||     |||    |  | ||||  ||||| ||||||||||||||||||||||||| ||| ||||||||| | ||||| |||   || |||||| | ||||||
--------------------------------------------------ggttaactgtatccttagaattgttggctt-ctcaaattaactatcaagccaattgaggctaattcttcatagattgaccatttcccttgtgccttaacagGCTAAGACCACCAAGAAGATTGTTCTGAGGCTCCAGTGCCAGGGTTGCAAACACGTATCCCAGCACCCAATCAAG

upper sequence: GRMZM2G103059_T01 (Zea mays), 3'ss of exon 2
lower sequence: Vv01s0011g02090.t01 (Vitis vinifera), 3'ss of exon 2
----------gtaatgcaacata-tctatttgattgtacttatacctttgtctgttttgatggtagcatgaatgtctagaaatatctgcgaattctaaatgcctgttga-gagaataatttgggatatgacaaatgtgattgtattaatacctttcagGCCAAGACCACCAAGAAGATTGTTCTGAAGCTGCAGTGCCAGAGCTGCAAGCACTACTCACAGCACGCCATCAAG
           |  |    |||  ||   ||  ||| | ||||   ||  |   | ||  |  ||    ||  |  |  |    | | | |||    | |    | | |  ||   || |    |||  |   ||     | | |    | |   ||||||||||| |||||||||||||| |||| ||| || |||||| | ||||| ||    || || ||| | ||||||
gtaaagaccctttctctggcattctcctcttccttgcaattatcaattgtttcatgtttcttataatgagagagcttgtaggatttttcaaatctgtagtagaagcttataagggcaaatccccatagcattgatccatctttttctcaaac---cagGCCAAGACAACCAAGAAGATTGTGCTGAGGCTTCAATGCCAGGGTTGCAAACATGTATCGCAACACCCAATCAAG

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|4826139|gb|AI667767.1|AI667767
EST:     GCAAGCAGTCAGGATATGGTGGTCAGACCAAGCCTGTCTTCCACAAGAAG                         GCCAAGACCACCAAGAAGATTGTTCTGAAGCTGCAGTGCCAGAGCTGCAAG
genomic: GCAAGCAGTCAGGACATGGTGGTCAGACCAAGCCTGTCTTCCACAAGAAGgtaatgcaac ... tacctttcagGCCAAGACCACCAAGAAGATTGTTCTGAAGCTGCAGTGCCAGAGCTGCAAG






















 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ctgttgagagaataatttgggatatgacaaatgtgattgtattaatacctttcagGCCAAGACCACCAAGAAGATTGTTCTGAAGCTGCAGTGCCAGAGCTGCAAGCACTACTCACAGCACGCCATCAAG
                                       tattaat  putative branch site (score: 2)
                                             tacctttc  CT-rich tract
                                 tgattgtattaata  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaatgcaacatatctatttgattgtacttatacctttgtctgttttgatggtagcatgaatgtctagaaatatctgcgaattctaaatgcctgttgagagaataatttgggatatgacaaatgtgattgtattaatacctttcagGCCAAGACCACCAAGAAGATTGTTCTGAAGCTGCAGTGCCAGAGCTGCAAGCACTACTCACAGCACGCCATCAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGCAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTGC