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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtacgaaatggccaggccgccagatctgtgcttcttcgcctatatcgatcgagtagaagttgacatgacatctcggacccgtgtctgtctgcatctgcgcagGAGAAGAACCACGGGTCGTTCGACTTCGTCTTCGTGGACGCCGACAAGGACAACTACCTCAACTACCACGAGCGGCTGCTGAAGCTGGTGAAGCTGGGCG

Basic information

species Zea mays
transcript GRMZM2G127948_T02
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G127948_T02 (Zea mays), 3'ss of exon 5
lower sequence: GLYMA02G11530.1 (Glycine max), 3'ss of exon 4
gtacgaaatggccaggccgccagatctgtgcttcttcgcctata-tcgatcgagtagaa-gttgacatgacatctcggacccgtgtctgtctgcatctgcgcagGAGAAGAACCACGGGTCGTTCGACTTCGTCTTCGTGGACGCCGACAAGGACAACTACCTCAACTACCACGAGCGGCTGCTGAAGCTGGTGAAGCTGGGCG
 ||  |||    || |       |||    ||   |     ||| || ||  ||  ||      | | |  |  | ||   ||  |  || ||       ||||||||||||||| |||   |  |||||| |||| |||||||| ||||||||||||||||||||||||||| || || || |  |||| || ||  | || |
-taaaaaaaatgcaagtttttccatc---actcaataaaaaataatcaatttagaggagtaaaaagagggtaattgggtagcgattgcgtgtggtgaaatgcagGAGAAGAACCATGGGAGCTATGACTTCATCTTTGTGGACGCAGACAAGGACAACTACCTCAACTACCACAAGAGGTTGATAGAGCTTGTCAAAGTTGGGG

upper sequence: GRMZM2G127948_T02 (Zea mays), 3'ss of exon 5
lower sequence: GLYMA07G33780.1 (Glycine max), 3'ss of exon 4
gtacgaaatggccaggccgccagatctgtgcttcttcgcctatatcgatcgagtagaagt-tgacatgacatctcggacccgtgtctgtctgcatctg--cgcagGAGAAGAACCACGGGTCGTTCGACTTCGTCTTCGTGGACGCCGACAAGGACAACTACCTCAACTACCACGAGCGGCTGCTGAAGCTGGTGAAGCTGGGCG
     || |      |   | | |  | | ||  |      | |   | | | | || |  | | |     |    |    |||  ||| ||         ||||||||||||||| ||    |  |||||| |||| || || || ||||||||||||||||||||||||||| || || || |  |||| || ||  | || |
-----aattctatgagagactaaaaatatactagtatttaaaaaaaaaacaattggaggagtaaaaaagggtaattgggtagtgattgtgtgtggtgaaatgcagGAGAAGAACCATGGAAGCTATGACTTCATCTTTGTTGATGCGGACAAGGACAACTACCTCAACTACCACAAGAGGTTGATAGAGCTTGTAAAAGTTGGGG

upper sequence: GRMZM2G127948_T02 (Zea mays), 3'ss of exon 5
lower sequence: GLYMA07G33780.2 (Glycine max), 3'ss of exon 4
gtacgaaatggccaggccgccagatctgtgcttcttcgcctatatcgatcgagtagaagt-tgacatgacatctcggacccgtgtctgtctgcatctg--cgcagGAGAAGAACCACGGGTCGTTCGACTTCGTCTTCGTGGACGCCGACAAGGACAACTACCTCAACTACCACGAGCGGCTGCTGAAGCTGGTGAA-GCTGGGCG--
        |      |   | | |  | | ||  |      | |   | | | | || |  | | |     |    |    |||  ||| ||         ||||||||||||||| ||    |  |||||| |||| || || || ||||||||||||||||||||||||||| || || || |  |||| || || | |||| |  
--------tctatgagagactaaaaatatactagtatttaaaaaaaaaacaattggaggagtaaaaaagggtaattgggtagtgattgtgtgtggtgaaatgcaggagAAGAACCATGGAAGCTATGACTTCATCTTTGTTGATGCGGACAAGGACAACTACCTCAACTACCACAAGAGGTTGATAGAGCTTGTAAAAGTTGGGGGCG

upper sequence: GRMZM2G127948_T02 (Zea mays), 3'ss of exon 5
lower sequence: Vv01s0010g03510.t01 (Vitis vinifera), 3'ss of exon 4
gtacgaaatggccaggccgccagatctgtgcttcttcgcctatatcgatcga--gtagaagttgacatgacatctcggacccgtgtctgtctgcatctgcgcagGAGAAGAACCACGGGTCGTTCGACTTCGTCTTCGTGGACGCCGACAAGGACAACTACCTCAACTACCACGAGCGGCTGCTGAAGCTGGTGAAGCTGGGCG
                        |  |||     || | ||  |||| | |  |  |   |  ||   ||| |||       ||  ||  || || || ||||| |||  |  | ||| | || ||||| |   | ||||| || || ||||| ||||||||||||||||| |||| |||||||||| |||| |   | || |
-----------------------gtaagtgtcctctc-cgtagctcgagccaccgctgccttcaaccaaacacctctc-tatttgaatgaatgaatgtgtgcagGGGAAAGAAGAAGGGACATTGGACTTTGCGATGGTGGATGCTGATAAGGAGAACTACCTCAACTACCATGAGCTGCTGCTGAAGTTGGTTAGAGTTGGAG

upper sequence: GRMZM2G127948_T02 (Zea mays), 3'ss of exon 5
lower sequence: Vv01s0010g03490.t01 (Vitis vinifera), 3'ss of exon 4
gtacgaaatggccaggccgccagatctgtgcttcttcgcctatatcgatcgagtagaagttgacatgacatctcggacccgtgtctgtctgcatctgcgcagGAGAAGAACCACGGGTCGTTCGACTTCGTCTTCGTGGACGCCGACAAGGACAACTACCTCAACTACCACGAGCGGCTGCTGAAGCTGGTGAAGCTGGGCG
                     |  | | | || | | ||      |      |         | |   |       |    ||  ||  || || || ||||| |||  |  | ||| | || || || |  || ||||| || || ||||| ||||||||||||||||| |||| |||||||||| |||| |   | || |
-------------------gtaagtgtcttctccgtagctcgggccaccgctgccttcaaccaaacacctctctaaatgaatgaatgaatgaatgtgtgcagGGGAACGAAGAAGGGACATTGGATTTTGCGTTTGTGGATGCTGATAAGGAGAACTACCTCAACTACCATGAGCTGCTGCTGAAGTTGGTTAGAGTTGGAG

upper sequence: GRMZM2G127948_T02 (Zea mays), 3'ss of exon 5
lower sequence: Vv01s0010g03470.t01 (Vitis vinifera), 3'ss of exon 2
gtacgaaatggccaggccgccagatctgtgcttcttcgcctatatcgatcgagtagaagttgacatgacatctcggacccgt--gtctgtctgcatctgcgcagGAGAAGAACCACGGGTCGTTCGACTTCGTCTTCGTGGACGCCGACAAGGACAACTACCTCAACTACCACGAGCGGCTGCTGAAGCTGGTGAAGCTGGGCG
                                     |    | |||     ||||  | || | | | | |    |||  |   | ||  || || || ||||| |||  |  | ||| | || || || |  || ||||| || || ||||| ||||||||||||||||| |||| |||||||||| |||| |   | || |
-------------------------------------gtaagtgtcgtctctgtagccgctgccttca-accaaacacctctcaatttgaatggatgtgtgcagGGGAACGAAGAAGGGACATTGGATTTTGCGTTTGTGGATGCTGATAAGGAGAACTACCTCAACTACCATGAGCTGCTGCTGAAGTTGGTTAGAGTTGGAG

upper sequence: GRMZM2G127948_T02 (Zea mays), 3'ss of exon 5
lower sequence: Vv07s0031g00350.t01 (Vitis vinifera), 3'ss of exon 4
gtacgaaatggccaggccgccagatctgtgcttcttcgcctatatcgatcgagtagaagttgacatgacatctcggacccgtgtctgtctgcatctgcgcagGAGAAGAACCACGGGTCGTTCGACTTCGTCTTCGTGGACGCCGACAAGGACAACTACCTCAACTACCACGAGCGGCTGCTGAAGCTGGTGAAGCTGGGCG
          |  ||  |   |   |       |  | || ||||    |  |    |  ||| |    ||        |     | ||  ||  |  |||||  ||| | || ||| | ||||| ||  | ||||||||||| ||||||||||||||||| ||||||||| |  ||||| |  | ||||| ||| | || |
----------gtaagtacaataatgcccctagcccactccaatattctccatgcctcatctga-acagaattgtaatttcaaaattatcaccaaat-tgcagGGAAAGTATCATGGGACATTCGATTTTATTTTCGTGGACGCTGACAAGGACAACTACCTGAACTACCACAAAAGGCTGATTGATCTGGTCAAGGTTGGAG

upper sequence: GRMZM2G127948_T02 (Zea mays), 3'ss of exon 5
lower sequence: Vv03s0063g00140.t01 (Vitis vinifera), 3'ss of exon 4
gtacgaaatggccaggccgccagatctgtgcttcttcgcctatatcgatcgagtagaagttgacatgacatctcggacccgtgtctgtctgcatctgcgcagGAGAAGAACCACGGGTCGTTCGACTTCGTCTTCGTGGACGCCGACAAGGACAACTACCTCAACTACCACGAGCGGCTGCTGAAGCTGGTGAAGCTGGGCG
||| |   |  | |   | |   |||    | |  |     || |  ||| |       |||| |  |  |    |||   ||| | | ||        |||| |||| | |||||||||||||||||| | ||||||||||| ||||||||||| || || ||||||||| || |  || |  |  |||||||| |||| |
gtaagct-tcacaaaaacccatcatccaaacattgt-----atttaaatccaaacatgattgaaacaagctaattgactt-tgtttctgtgatgaaaaacagGGGAAGTATCACGGGTCGTTCGACTTCATATTCGTGGACGCAGACAAGGACAATTATCTGAACTACCACAAGAGATTGATCGATTTGGTGAAGGTGGGGG

upper sequence: GRMZM2G127948_T02 (Zea mays), 3'ss of exon 5
lower sequence: EFJ11728 (Selaginella moellendorffii), 3'ss of exon 4
gtacgaaatggccaggccgccagatctgtgcttcttcgcctatatcgatcgagtagaagttgacatgacatctcggacccgtgtctgtctgcatctgcgcagGAGAAGAACCACGGGTCGTTCGACTTCGTCTTCGTGGACGCCGACAAGGACAACTACCTCAACTACCACGAGCGGCTGCTGAAGCTGGTGAAGCTGGGCG
                           ||     |||    |||    |    |  |  ||  | |||     ||   |  || ||| |    ||  ||||||||  ||| || ||  ||||||||||| |||| ||||| || ||||||||||| ||| | ||||||||| || || || |     |||| ||  | || |
---------------------------gtaagctttca---atacaacttttctttatcttaccttgaaccaacga--caatg-ctgacactttcctcgcagGAGGCGAATCATGGCGCGTTCGACTTCATCTTTGTGGATGCTGACAAGGACAATTACTTGAACTACCACAAGAGGTTGATCTCTTTGGTTAAAGTCGGAG

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|149076213|gb|EE164810.2|EE164810
EST:     CTCCCCGTCCTCGACGACCTCATCGCGGAG                         GAGAAGAACCACGGGTCGTTCGACTTCGTCTTCGTGGACGCCGACAAGGAC
genomic: CTCCCCGTCCTCGACGACCTCATCGCGGAGgtacgaaatg ... atctgcgcagGAGAAGAACCACGGGTCGTTCGACTTCGTCTTCGTGGACGCCGACAAGGAC
EST: gi|14245569|gb|BG874151.1|BG874151
EST:     ACCTCATCGCGGAG                         GAGAAGAACCACGGGTCGTTCGACTTCGTCTTCGTGGACGCCGACAAGGAC
genomic: ACCTCATCGCGGAGgtacgaaatg ... atctgcgcagGAGAAGAACCACGGGTCGTTCGACTTCGTCTTCGTGGACGCCGACAAGGAC
EST: gi|78021612|gb|DV489999.1|DV489999
EST:     CTCCCCGTCCTCGACGACCTCATCGCGGAG                         GAGAAGAACCACGGGTCGTTCGACTTCGTCTTCGTGGACGCCGACAAGGAC
genomic: CTCCCCGTCCTCGACGACCTCATCGCGGAGgtacgaaatg ... atctgcgcagGAGAAGAACCACGGGTCGTTCGACTTCGTCTTCGTGGACGCCGACAAGGAC
EST: gi|149076214|gb|EE164811.2|EE164811
EST:     CTCCCCGTCCTCGACGACCTCATCGCGGAG                         GAGAAGAACCACGGGTCGTTCGACTTCGTCTTCGTGGACGCCGACAAGGAC
genomic: CTCCCCGTCCTCGACGACCTCATCGCGGAGgtacgaaatg ... atctgcgcagGAGAAGAACCACGGGTCGTTCGACTTCGTCTTCGTGGACGCCGACAAGGAC
EST: gi|5499345|gb|AI855212.1|AI855212
EST:     CGACCTCATCGCGGAG                         GAGAAGAACCACGGGTCGTTCGACTTCGTCTTCGTGGACGCCGACAAGGAC
genomic: CGACCTCATCGCGGAGgtacgaaatg ... atctgcgcagGAGAAGAACCACGGGTCGTTCGACTTCGTCTTCGTGGACGCCGACAAGGAC

RNA-Seq data


 ATGC   Supported by RNA-Seq exonic block that spans over the splice site

 atgs   Truncated intron sequence

Each block is as long as the maximal overhang of any read spanning the junction.
The score is the number of alignments spanning the junction.


Found data for 6 RNA-Seq libraries.


Block sizes: 45 (upstream exon), 45 (downstream exon)
Score: 74

CTCCCCGTCCTCGACGACCTCATCGCGGAGgtacgaaatg ... atctgcgcagGAGAAGAACCACGGGTCGTTCGACTTCGTCTTCGTGGACGCCGACAAGGACAACTACCTCAACTACCACGAGCGGCTGCTGAAGCTGGTGAAGCTGGGCG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 337

CTCCCCGTCCTCGACGACCTCATCGCGGAGgtacgaaatg ... atctgcgcagGAGAAGAACCACGGGTCGTTCGACTTCGTCTTCGTGGACGCCGACAAGGACAACTACCTCAACTACCACGAGCGGCTGCTGAAGCTGGTGAAGCTGGGCG


Block sizes: 13 (upstream exon), 49 (downstream exon)
Score: 55

CTCCCCGTCCTCGACGACCTCATCGCGGAGgtacgaaatg ... atctgcgcagGAGAAGAACCACGGGTCGTTCGACTTCGTCTTCGTGGACGCCGACAAGGACAACTACCTCAACTACCACGAGCGGCTGCTGAAGCTGGTGAAGCTGGGCG


Block sizes: 47 (upstream exon), 45 (downstream exon)
Score: 190

CTCCCCGTCCTCGACGACCTCATCGCGGAGgtacgaaatg ... atctgcgcagGAGAAGAACCACGGGTCGTTCGACTTCGTCTTCGTGGACGCCGACAAGGACAACTACCTCAACTACCACGAGCGGCTGCTGAAGCTGGTGAAGCTGGGCG


Block sizes: 27 (upstream exon), 49 (downstream exon)
Score: 107

CTCCCCGTCCTCGACGACCTCATCGCGGAGgtacgaaatg ... atctgcgcagGAGAAGAACCACGGGTCGTTCGACTTCGTCTTCGTGGACGCCGACAAGGACAACTACCTCAACTACCACGAGCGGCTGCTGAAGCTGGTGAAGCTGGGCG


Block sizes: 47 (upstream exon), 45 (downstream exon)
Score: 314

CTCCCCGTCCTCGACGACCTCATCGCGGAGgtacgaaatg ... atctgcgcagGAGAAGAACCACGGGTCGTTCGACTTCGTCTTCGTGGACGCCGACAAGGACAACTACCTCAACTACCACGAGCGGCTGCTGAAGCTGGTGAAGCTGGGCG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atcgagtagaagttgacatgacatctcggacccgtgtctgtctgcatctgcgcagGAGAAGAACCACGGGTCGTTCGACTTCGTCTTCGTGGACGCCGACAAGGACAACTACCTCAACTACCACGAGCGGCTGCTGAAGCTGGTGAAGCTGGGCG
          agttgac  putative branch site (score: 314)
















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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtacgaaatggccaggccgccagatctgtgcttcttcgcctatatcgatcgagtagaagttgacatgacatctcggacccgtgtctgtctgcatctgcgcagGAGAAGAACCACGGGTCGTTCGACTTCGTCTTCGTGGACGCCGACAAGGACAACTACCTCAACTACCACGAGCGGCTGCTGAAGCTGGTGAAGCTGGGCG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCTG