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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CGTCCTCCAACCTGATCCACGACTGCGACGAGGTCTTCAACTACTGGGAGCCCCTCCACTTCCTCCTCTACCGCTCCGGCTTCCAGACATGGGAGTACAGgtagcctctccgacctcacccccatagacccgcctgcgcctgccatttcggctacttgatgctcctgggcgtactggcagagtttggacttgtgctctga...

Basic information

species Zea mays
transcript GRMZM2G051262_T01
intron # 1
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G051262_T01 (Zea mays), 5'ss of exon 1
lower sequence: LOC_Os01g11070.1 (Oryza sativa), 5'ss of exon 1
CGTCCTCCAACCTGATCCACGACTGCGACGAGGTCTTCAACTACTGGGAGCCCCTCCACTTCCTCCTCTACCGCTCCGGCTTCCAGACATGGGAGTACAGgtagc----ctctccgacctcaccc-ccatagacccgcctgcgcctgc-catttcggctacttgatgctcctgggcgtactggcagagtt-tggacttgtgctctga
|||||||||||||||||||||||||||||||||| ||||||||||||||||||||||||||||||||||||||||||||||||||||| |||||||||||||  |     | ||   | |||| | || || ||    |     |||  || ||||  |   ||||||||   |  |  | ||| || |   ||||  |   |    
CGTCCTCCAACCTGATCCACGACTGCGACGAGGTGTTCAACTACTGGGAGCCCCTCCACTTCCTCCTCTACCGCTCCGGCTTCCAGACCTGGGAGTACAGgtctcgcttttttctcgcttcactctccctaaactaaaccctagctgtacagttcgttt---tgatgctc---gatgcgcgggcggaatcgcggaccgggattgca-

upper sequence: GRMZM2G051262_T01 (Zea mays), 5'ss of exon 1
lower sequence: GLYMA12G35830.1 (Glycine max), 5'ss of exon 1
CGTCCTCCAACCTGATCCACGACTGCGACGAGGTCTTCAACTACTGGGAGCCCCTCCACTTCCTCCTCTACC----GCTCCGGCTTCCAGACATGGGAGTACAGg-tagcctctccgacctcacccccatagacccgcctgcgcctgccatttcggctacttgatgctcctgggcgtactggcagagtttggacttgtgctctga----
  |    || |  |   | ||    || || | ||    || |   | | |     |    |        ||        |||     | | | |   |    || | |  | | |    |    | | | ||         |      | | |  |  |      |  |   |  | | | |   || |  | ||   ||  ||    
--TGAGGCAGC--GGCGCTCGGAGCCGTCG-GATCCGTCACCATCAGAACCGTACACGAAGCTGGACAAGCCCGAGAAAGCGGAGGAGAAAGACGAAGGCTTGGGgtgggtttttccgtttgtggctcttggatt-attgaggtacatgagtgccacctccaacatcatccacgattgc-gacgaggtcttcaatt--actgggagccc

upper sequence: GRMZM2G051262_T01 (Zea mays), 5'ss of exon 1
lower sequence: GLYMA13G34570.1 (Glycine max), 5'ss of exon 1
CGTCCTCCAACCTGATCCACGACTGCGACGAGGTCTTCAACTACTGGGAGCCCCTCCACTTCCTCCTCTACCGCTCCGGCTTCCAGACATGGGAGTACAGgtagcctctccgac--ctcacccccatagacccgcctgc--gcctgccatttcggctacttgatgc-tcctgggcgtactggcagagtttggacttgtgctctga
|  |||||||| | |||||||| ||||||||||||||||| ||||||||||| || || ||||| ||||||   || || |||||||||||||| |||||||    |     |   |||  |  | |   |     ||   |  | |  ||| ||  |  |||||  ||  ||| | |  |  | ||||| || || |       
CCACCTCCAACATCATCCACGATTGCGACGAGGTCTTCAATTACTGGGAGCCTCTTCATTTCCTTCTCTACAAATCTGGATTCCAGACATGGGAATACAGgttctgttctgtattgctcttcttcttcttcttttttgttggggttcagttttggggagatgatgggtcaagggagaagagagaaagttttgatttttat-----

upper sequence: GRMZM2G051262_T01 (Zea mays), 5'ss of exon 1
lower sequence: Vv19s0014g01410.t01 (Vitis vinifera), 5'ss of exon 1
CGTCCTCCAACCTGATCCACGACTGCGACGAGGTCTTCAACTACTGGGAGCCCCTCCACTTCCTCCTCTACCGCTCCGGCTTCCAGACATGGGAGTACAGgtagcctctccgacctcacccccatagacccgcctgcgcctgccat-ttcggctacttgatgctcctgggcgtactggcagagtttggacttgtgctctga
|  | || ||  | |||||||||||||| ||||| |||||||| |||||||| ||||||||||||||||||   || || ||||| || ||||| || |||||         |    |       |   | |  | |   | |||  ||  |  | ||  |  |  ||   || || |  ||         | || |   |
CCACATCGAATATCATCCACGACTGCGATGAGGTTTTCAACTATTGGGAGCCTCTCCACTTCCTCCTCTACAAATCTGGTTTCCAAACTTGGGAATATAGgtaaaaaaaaaaaaaaaaaatttcaatttcagatttctttttccacattttgtaattttgtagtt-tgcttgtgctagtggaaacgatggatttgtttgaa

upper sequence: GRMZM2G051262_T01 (Zea mays), 5'ss of exon 1
lower sequence: PP1S478_15V6.1 (Physcomitrella patens), 5'ss of exon 1
CGTCCTCCAACCTGATCCACGACTGCGACGAGGTCTTCAACTACTGGGAGCCCCTCCACTTCCTCCTCTACCGCTCCGGCTTCCAGACATGGGAGTACAGgtagcc--tctccgacct-cacccccatagacccgcctgcgcctgccatttcggctacttgatgctcctgggcgtactggcagagtttggacttgtgctctga----
    ||  ||    || ||||||||||||||||| ||||| ||||||||||| || |||| ||| || |||   ||||| ||||| || |||||||||||||| |   ||  ||  || |     || |||   |   | ||||| | ||| ||||      |    |       ||      |  || || || |  |   |    
TTGTCTATAATAATATTCACGACTGCGACGAGGTGTTCAATTACTGGGAGCCGCTTCACTACCTTCTTTACAAGTCCGGGTTCCAAACCTGGGAGTACAGgtaactaatcgtcgttctactgaatcagagaga-gggagagcctgtcgttttggct------tagggcgaaattcacctatgaaaattcgatttctttttgaaacaa

upper sequence: GRMZM2G051262_T01 (Zea mays), 5'ss of exon 1
lower sequence: EFJ13347 (Selaginella moellendorffii), 5'ss of exon 1
CGTCCTCCAACCTGATCCACGACTGCGACGAGGTCTTCAACTACTGGGAGCCCCTCCACTTCCTCCTCTACCGCTCCGGCTTCCAGACATGGGAGTACAGgtagcctctccgacctcacccccatagacccgcctgcgcctgccatttcggctacttgatgctcctgggcgtactggcagagtttggacttgtgctctga
||  ||||||| |  | ||||||||||||||||| ||||| ||||||||||| || || || || |||||  | || || || || || |||||||||||||               | |   | |||   |  |  |    |    |    || |||  | | |  |     ||||   ||                  
CGAGCTCCAACATCGTACACGACTGCGACGAGGTTTTCAATTACTGGGAGCCGCTGCATTTTCTTCTCTATGGATCGGGATTTCAAACTTGGGAGTACAGgtga--------gtgagagctttagaga---gtgtctgttctctcgctaaaataattggagtttc--gtttctctggactag------------------

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|28909967|gb|CB331189.1|CB331189
EST:     CCCCTCCACTTCCTCCTCTACCGCTCCGGCTTCCAGACATGGGAGTACAG                         TTCCGACTTTGCTCTTCGGTCATATTTGTACCTTTTCTTTCATGCTCTTGT
genomic: CCCCTCCACTTCCTCCTCTACCGCTCCGGCTTCCAGACATGGGAGTACAGgtagcctctc ... tttattgcagTTCCGACTTTGCTCTTCGGTCATATTTGTACCTTTTCTTTCATGCTCTTGT
EST: gi|148995029|gb|EE034347.2|EE034347
EST:     CCCCTCCACTTCCTCCTCTACCGCTCCGGCTTCCAGACATGGGAGTACAG                         TTCCGACTTTGCTCTTCGGTCATATTTGTACCTTTTCTTTCATGCTCTTGT
genomic: CCCCTCCACTTCCTCCTCTACCGCTCCGGCTTCCAGACATGGGAGTACAGgtagcctctc ... tttattgcagTTCCGACTTTGCTCTTCGGTCATATTTGTACCTTTTCTTTCATGCTCTTGT
EST: gi|211188227|gb|FK983678.1|FK983678
EST:     CCCCTCCACTTCCTCCTCTACCGCTCCGGCTTCCAGACATGGGAGTACAG                         TTCCGACTTTGCTCTTCGGTCATATTTGTACCTTTTCTTTCATGCTCTTGT
genomic: CCCCTCCACTTCCTCCTCTACCGCTCCGGCTTCCAGACATGGGAGTACAGgtagcctctc ... tttattgcagTTCCGACTTTGCTCTTCGGTCATATTTGTACCTTTTCTTTCATGCTCTTGT
EST: gi|76281865|gb|DV021433.1|DV021433
EST:     CCCCTCCACTTCCTCCTCTACCGCTCCGGCTTCCAGACATGGGAGTACAG                         TTCCGACTTTGCTCTTCGGTCATATTTGTACCTTTTCTTTCATGCTCTTGT
genomic: CCCCTCCACTTCCTCCTCTACCGCTCCGGCTTCCAGACATGGGAGTACAGgtagcctctc ... tttattgcagTTCCGACTTTGCTCTTCGGTCATATTTGTACCTTTTCTTTCATGCTCTTGT
EST: gi|211188226|gb|FK983677.1|FK983677
EST:     CCCCTCCACTTCCTCCTCTACCGCTCCGGCTTCCAGACATGGGAGTACAG                         TTCCGACTTTGCTCTTCGGTCATATTTGTACCTTTTCTTTCATGCTCTTGT
genomic: CCCCTCCACTTCCTCCTCTACCGCTCCGGCTTCCAGACATGGGAGTACAGgtagcctctc ... tttattgcagTTCCGACTTTGCTCTTCGGTCATATTTGTACCTTTTCTTTCATGCTCTTGT
EST: gi|211188228|gb|FK983679.1|FK983679
EST:     CCCCTCCACTTCCTCCTCTACCGCTCCGGCTTCCAGACATGGGAGTACAG                         TTCCGACTTTGCTCTTCGGTCATATTTGTACCTTTTCTTTCATGCTCTTGT
genomic: CCCCTCCACTTCCTCCTCTACCGCTCCGGCTTCCAGACATGGGAGTACAGgtagcctctc ... tttattgcagTTCCGACTTTGCTCTTCGGTCATATTTGTACCTTTTCTTTCATGCTCTTGT
EST: gi|211188231|gb|FK983682.1|FK983682
EST:     CCCCTCCACTTCCTCCTCTACCGCTCCGGCTTCCAGACATGGGAGTACAG                         TTCCGACTTTGCTCTTCGGTCATATTTGTACCTTTTCTTTCATGCTCTTGT
genomic: CCCCTCCACTTCCTCCTCTACCGCTCCGGCTTCCAGACATGGGAGTACAGgtagcctctc ... tttattgcagTTCCGACTTTGCTCTTCGGTCATATTTGTACCTTTTCTTTCATGCTCTTGT
EST: gi|74233286|gb|DT641200.1|DT641200
EST:     CCCCTCCACTTCCTCCTCTACCGCTCCGGCTTCCAGACATGGGAGTACAG                         TTCCGACTTTGCTCTTCGGTCATATTTGTACCTTTTCTTTCATGCTCTTGT
genomic: CCCCTCCACTTCCTCCTCTACCGCTCCGGCTTCCAGACATGGGAGTACAGgtagcctctc ... tttattgcagTTCCGACTTTGCTCTTCGGTCATATTTGTACCTTTTCTTTCATGCTCTTGT
EST: gi|211188225|gb|FK983676.1|FK983676
EST:     CCCCTCCACTTCCTCCTCTACCGCTCCGGCTTCCAGACATGGGAGTACAG                         TTCCGACTTTGCTCTTCGGTCATATTTGTACCTTTTCTTTCATGCTCTTGT
genomic: CCCCTCCACTTCCTCCTCTACCGCTCCGGCTTCCAGACATGGGAGTACAGgtagcctctc ... tttattgcagTTCCGACTTTGCTCTTCGGTCATATTTGTACCTTTTCTTTCATGCTCTTGT
EST: gi|211190623|gb|FK983686.1|FK983686
EST:     CCCCTCCACTTCCTCCTCTACCGCTCCGGCTTCCAGACATGGGAGTACAG                         TTCCGACTTTGCTCTTCGGTCATATTTGTACCTTTTCTTTCATGCTCTTGT
genomic: CCCCTCCACTTCCTCCTCTACCGCTCCGGCTTCCAGACATGGGAGTACAGgtagcctctc ... tttattgcagTTCCGACTTTGCTCTTCGGTCATATTTGTACCTTTTCTTTCATGCTCTTGT
EST: gi|71772097|gb|DR970034.1|DR970034
EST:     CCCCTCCACTTCCTCCTCTACCGCTCCGGCTTCCAGACATGGGAGTACAG                         TTCCGACTTTGCTCTTCGGTCATATTTGTACCTTTTCTTTCATGCTCTTGT
genomic: CCCCTCCACTTCCTCCTCTACCGCTCCGGCTTCCAGACATGGGAGTACAGgtagcctctc ... tttattgcagTTCCGACTTTGCTCTTCGGTCATATTTGTACCTTTTCTTTCATGCTCTTGT
EST: gi|211188230|gb|FK983681.1|FK983681
EST:     CCCCTCCACTTCCTCCTCTACCGCTCCGGCTTCCAGACATGGGAGTACAG                         TTCCGACTTTGCTCTTCGGTCATATTTGTACCTTTTCTTTCATGCTCTTGT
genomic: CCCCTCCACTTCCTCCTCTACCGCTCCGGCTTCCAGACATGGGAGTACAGgtagcctctc ... tttattgcagTTCCGACTTTGCTCTTCGGTCATATTTGTACCTTTTCTTTCATGCTCTTGT
EST: gi|211190621|gb|FK983684.1|FK983684
EST:     CCCCTCCACTTCCTCCTCTACCGCTCCGGCTTCCAGACATGGGAGTACAG                         TTCCGACTTTGCTCTTCGGTCATATTTGTACCTTTTCTTTCATGCTCTTGT
genomic: CCCCTCCACTTCCTCCTCTACCGCTCCGGCTTCCAGACATGGGAGTACAGgtagcctctc ... tttattgcagTTCCGACTTTGCTCTTCGGTCATATTTGTACCTTTTCTTTCATGCTCTTGT
EST: gi|91054950|gb|EB165368.1|EB165368
EST:     CCCCTCCACTTCCTCCTCTACCGCTCCGGCTTCCAGACATGGGAGTACAG                         TTCCGACTTTGCTCTTCGGTCATATTTGTACCTTTTCTTTCATGCTCTTGT
genomic: CCCCTCCACTTCCTCCTCTACCGCTCCGGCTTCCAGACATGGGAGTACAGgtagcctctc ... tttattgcagTTCCGACTTTGCTCTTCGGTCATATTTGTACCTTTTCTTTCATGCTCTTGT
EST: gi|149100385|gb|EE186457.2|EE186457
EST:     CCCCTCCACTTCCTCCTCTACCGCTCCGGCTTCCAGACATGGGAGTACAG                         TTCCGACTTTGCTCTTCGGTCATATTTGTACCTTTTCTTTCATGCTCTTGT
genomic: CCCCTCCACTTCCTCCTCTACCGCTCCGGCTTCCAGACATGGGAGTACAGgtagcctctc ... tttattgcagTTCCGACTTTGCTCTTCGGTCATATTTGTACCTTTTCTTTCATGCTCTTGT
EST: gi|211190622|gb|FK983685.1|FK983685
EST:     CCCCTCCACTTCCTCCTCTACCGCTCCGGCTTCCAGACATGGGAGTACAG                         TTCCGACTTTGCTCTTCGGTCATATTTGTACCTTTTCTTTCATGCTCTTGT
genomic: CCCCTCCACTTCCTCCTCTACCGCTCCGGCTTCCAGACATGGGAGTACAGgtagcctctc ... tttattgcagTTCCGACTTTGCTCTTCGGTCATATTTGTACCTTTTCTTTCATGCTCTTGT

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 4 RNA-Seq libraries.


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 148

CGTCCTCCAACCTGATCCACGACTGCGACGAGGTCTTCAACTACTGGGAGCCCCTCCACTTCCTCCTCTACCGCTCCGGCTTCCAGACATGGGAGTACAGgtagcctctc ... tttattgcagTTCCGACTTTGCTCTTCGGTCATATTTGTACCTTTTCTTTCATGCTCTTGTAGCTGGGCCTGCTTCATTGATCTTTGGTGAGCATAAG


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 69

CGTCCTCCAACCTGATCCACGACTGCGACGAGGTCTTCAACTACTGGGAGCCCCTCCACTTCCTCCTCTACCGCTCCGGCTTCCAGACATGGGAGTACAGgtagcctctc ... tttattgcagTTCCGACTTTGCTCTTCGGTCATATTTGTACCTTTTCTTTCATGCTCTTGTAGCTGGGCCTGCTTCATTGATCTTTGGTGAGCATAAG


Block sizes: 47 (upstream exon), 49 (downstream exon)
Score: 105

CGTCCTCCAACCTGATCCACGACTGCGACGAGGTCTTCAACTACTGGGAGCCCCTCCACTTCCTCCTCTACCGCTCCGGCTTCCAGACATGGGAGTACAGgtagcctctc ... tttattgcagTTCCGACTTTGCTCTTCGGTCATATTTGTACCTTTTCTTTCATGCTCTTGTAGCTGGGCCTGCTTCATTGATCTTTGGTGAGCATAAG


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 160

CGTCCTCCAACCTGATCCACGACTGCGACGAGGTCTTCAACTACTGGGAGCCCCTCCACTTCCTCCTCTACCGCTCCGGCTTCCAGACATGGGAGTACAGgtagcctctc ... tttattgcagTTCCGACTTTGCTCTTCGGTCATATTTGTACCTTTTCTTTCATGCTCTTGTAGCTGGGCCTGCTTCATTGATCTTTGGTGAGCATAAG


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CGTCCTCCAACCTGATCCACGACTGCGACGAGGTCTTCAACTACTGGGAGCCCCTCCACTTCCTCCTCTACCGCTCCGGCTTCCAGACATGGGAGTACAGgtagcctctccgacctcacccccatagacccgcctgcgcctgccatttcggctacttgatgctcctgggcgtactggcagagtttggacttgtgctctga

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTCCTC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - caccccc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -acccgcc