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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatacaagtaggagcacatacttaataatttttttgtagtatctgctttatagcagagcttctatcactatgatctatttttttctcatatctgcttttgtatttttgtttagGTTGATGACTTGGAAGAAGTCAGTGAGTACTACCAAAATAGAGGATGCTTCAATGAACTCATTGCTCTCATGGAGAGTGGTCTTGGACTAGAACGTGCAC

Basic information

species Zea mays
transcript GRMZM2G325285_T01
intron # 14
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G325285_T01 (Zea mays), 3'ss of exon 14
lower sequence: GLYMA02G39360.1 (Glycine max), 3'ss of exon 24
gtatacaagtaggagcacatacttaataatttttttgtagtatctgctttatagcagagcttctatcactatgatctatttttttctcatatctgcttttgtatttttgtttagGTTGATGACTTGGAAGAAGTCAGTGAGTACTACCAAAATAGAGGATGCTTCAATGAACTCATTGCTCTCATGGAGAGTGGTCTTGGACTAGAACGTGCAC
         | ||   |  ||    |  |||       |||  | | |  | ||  ||  ||   |   |||  ||| || |||  | |    | || || |||| || |  |||| ||||| |||||||| || |||||||  ||||| || ||||||||||| |||||||| ||  |||| ||||||||||| |||||||| || ||||| |
--------attgggaaatgta---gaacattggcaacaagtggcagatagacagttga--ttagtttgttattttctgttgtttgattactaattctctt-tattattatgaagGTGGATGATTTGGAAGAGGTTAGTGAGTTTTACCAGAACAGAGGATGCTTTAATGAACTGATATCTCTAATGGAGAGTGGACTTGGACTGGAGCGTGCCC

upper sequence: GRMZM2G325285_T01 (Zea mays), 3'ss of exon 14
lower sequence: GLYMA18G02960.1 (Glycine max), 3'ss of exon 23
gtatacaagtaggagcacatacttaataatttttttgtagtatctgctttatagcagagcttctatcactatgatctatttttttctcatatctgcttttgtatttttgtttagGTTGATGACTTGGAAGAAGTCAGTGAGTACTACCAAAATAGAGGATGCTTCAATGAACTCATTGCTCTCATGGAGAGTGGTCTTGGACTAGAACGTGCAC
      |   |  |  | || ||   | |   ||   ||  ||||||  | |   |   ||| ||    |   |    || || | |||  | |  || || ||||     ||||| |||||||||||||| |||||||| || |||||||||||||| ||||||||||| || ||  | || |||||||||||| | ||| ||||||| ||||
------agagaaaaaaaaatgct--gtgagcattacttaa-atctgcagtttgttac--cttatagtctttccaatgcttattatgtcaattttcattgtgaatttg---gtagGTGGATGACTTGGAAGAGGTCAGTGAATATTACCAAAATAGAGGTTGCTTCAATGAGCTAATATCGCTTATGGAGAGTGGTTTAGGATTAGAACGGGCAC

upper sequence: GRMZM2G325285_T01 (Zea mays), 3'ss of exon 14
lower sequence: GLYMA01G38580.1 (Glycine max), 3'ss of exon 24
gtatacaagtaggagcaca-tacttaataatttttttgtagtatctgctttatagcagagcttctatcactatgatctatttttttctcatatctgct-tttgtatttttgtttagGTTGATGACTTGGAAGAAGTCAGTGAGTACTACCAAAATAGAGGATGCTTCAATGAACTCATTGCTCTCATGGAGAGTGGTCTTGGACTAGAACGTGCAC
         ||| |||| | |||| || |    |     |  | ||  || || ||   |  |||| |  | ||| |    || |    |||  | || | ||| || |  |  |||| ||||| ||||| || || || |||||||| || || |||||||||||||||||||||||  |||| |||||||||||  | ||| | || |||||||
---------tagtagcaaaatactaaaaacaagtgacagaaaaact-tttgattgctttg--tctaaccttttgacc----ttgtctgaatacttactatctgttttatattgaagGTGGATGATTTGGAGGAGGTTAGCGAGTACTATCAGAACAGAGGATGCTTCAATGAACTCATATCTCTAATGGAGAGTGGGTTAGGATTGGAGCGTGCAC

upper sequence: GRMZM2G325285_T01 (Zea mays), 3'ss of exon 14
lower sequence: GLYMA14G37510.1 (Glycine max), 3'ss of exon 22
gtatacaagtaggagcacatacttaataatttttttgtagtatctgctttatagcagagcttctatcactatgatctatttttttctcatatctgcttttgtatttttgtttagGTTGATGACTTGGAAGAAGTCAGTGAGTACTACCAAAATAGAGGATGCTTCAATGAACTCATTGCTCTCATGGAGAGTGGTCTTGGACTAGAACGTGCAC
         | ||   |  ||    |  |||       |||  | | |  |  |  ||  ||   |   |||  ||| || |||         | || || |||| || |  |||| ||||| |||||||| || |||||||  || || || ||||||||||| |||||||||||  |||| ||||||||||| |||||||| || ||||| |
--------attgggaaatgta---gaacattggcaacaagtgccagatagactgttga--ttagtttgttattttctgttgtttgactgctaattctctt-tattattatgaagGTGGATGATTTGGAAGAGGTTAGTGAGTTTTATCAGAACAGAGGATGCTTTAATGAACTCATATCTCTAATGGAGAGTGGACTTGGACTGGAGCGTGCCC

upper sequence: GRMZM2G325285_T01 (Zea mays), 3'ss of exon 14
lower sequence: GLYMA11G35460.1 (Glycine max), 3'ss of exon 23
gtatacaagtaggagcacatact-taataatttttttgtagtatctgctttatagcagagcttctatcactatgatctatttttttctcatatctgcttttgtatttttgtttagGTTGATGACTTGGAAGAAGTCAGTGAGTACTACCAAAATAGAGGATGCTTCAATGAACTCATTGCTCTCATGGAGAGTGGTCTTGGACTAGAACGTGCAC
       || || |  | || || | |  |||  ||    | ||||||  | | |   | ||| ||    |   |    || || | |||  | |  || || ||||     ||||| |||||||||||||| |||||||| || |||||||||||||| ||||||||||| || ||  | ||||||||||||||| | ||| ||||||| ||||
-------aggagaaaaaaatgctgtgagcattactt----gaatctgcagt-ttgtttaccttatagtctttccaatgcttattatgtcaattttcattgtgaatttg---gtagGTGGATGACTTGGAAGAGGTCAGTGAATATTACCAAAATAGAGGTTGCTTCAATGAGCTAATATCCCTCATGGAGAGTGGTTTAGGATTAGAACGGGCAC

upper sequence: GRMZM2G325285_T01 (Zea mays), 3'ss of exon 14
lower sequence: GLYMA02G42560.1 (Glycine max), 3'ss of exon 24
gtatacaagtaggagcacatacttaataatttttttgtagtatctgctttatagcagagcttctatcactatgatctatttttttctcatatctgcttttgtatttttgtttagGTTGATGACTTGGAAGAAGTCAGTGAGTACTACCAAAATAGAGGATGCTTCAATGAACTCATTGCTCTCATGGAGAGTGGTCTTGGACTAGAACGTGCAC
           ||      | |||  || |||     || |       |  | | || | |  |||    |   |||| |  ||  |      |  ||||   |  || |  |||| ||||||||||||||||||||||| || |||||||||||||| ||||||||||| || ||  |||| |||||||||||| | ||  ||||||| ||||
-----------gggtgttttgcttggta-tttgaacttaatgctgatctgctggtagtgatcttattg--aatttctaatgcttattgcgtcatttttttaattaattttaaagGTGGATGACTTGGAAGAAGTCAGTGAATATTACCAAAATAGAGGTTGCTTCAATGAGCTAATATCTCTGATGGAGAGTGGTTTAGGGTTAGAACGGGCAC

upper sequence: GRMZM2G325285_T01 (Zea mays), 3'ss of exon 14
lower sequence: GLYMA11G06720.1 (Glycine max), 3'ss of exon 24
gtatacaagtaggagcacatacttaataatttttttgtagtatctgctttatagcagagcttctatcactatgatctatttttttctcatatctgcttttgtatttttgtttagGTTGATGACTTGGAAGAAGTCAGTGAGTACTACCAAAATAGAGGATGCTTCAATGAACTCATTGCTCTCATGGAGAGTGGTCTTGGACTAGAACGTGCAC
     | ||||| |  | ||||| ||  |  |    | |  |  |  || || ||      |||| |  | ||   |  | |     |  |    || || ||| ||     |||| ||||| ||||| || || || ||||| || ||||| |||||||||||||||||||||||  |||| |||||||||||  | ||| | || |||||||
-----ctagtagca--aaatactaaaacaagtgacagaaaaactt--ttgattgcttta--tctaaccttttggcgttgtctgaataccaactatctgttatatattga---agGTGGATGATTTGGAGGAGGTTAGCGAGTATTATCAAAACAGAGGATGCTTCAATGAACTCATATCTCTAATGGAGAGTGGGTTAGGATTGGAGCGTGCAC

upper sequence: GRMZM2G325285_T01 (Zea mays), 3'ss of exon 14
lower sequence: GLYMA14G06340.1 (Glycine max), 3'ss of exon 24
gtatacaagtaggagcacatacttaataatttttttgtagtatctgctttatagcagagcttctatcactatgatctatttttttctcatatctgcttttgtatttttgtttagGTTGATGACTTGGAAGAAGTCAGTGAGTACTACCAAAATAGAGGATGCTTCAATGAACTCATTGCTCTCATGGAGAGTGGTCTTGGACTAGAACGTGCAC
           ||      | |||  | || |     || | |    ||  ||  || | |  |||    ||     ||  || |  | |   |  |||| | |  ||   ||||| ||||||||||||||||||||||| || |||||||| ||||| ||||||||||| |||||  ||||||||||||||||| | ||  ||||||| ||||
-----------gggtgttgtgcttg-ttatatgaacttaatgttgatttgctactagtgatcttattga-atttctaatgcttattgcgtcattttttttat-taatttcatagGTGGATGACTTGGAAGAAGTCAGTGAATATTACCAAAACAGAGGTTGCTTCAATGAGCTCATATCTCTCATGGAGAGTGGTTTAGGGTTAGAACGGGCAC

upper sequence: GRMZM2G325285_T01 (Zea mays), 3'ss of exon 14
lower sequence: AT3G08530.1 (Arabidopsis thaliana), 3'ss of exon 24
gtatacaagtaggagcacata-cttaataattttt--ttgtagtatctgctttatagcagagc-----ttctatcactatgatctatttttttctcatatctgcttttgtatttttgtttagGTTGATGACTTGGAAGAAGTCAGTGAGTACTACCAAAATAGAGGATGCTTCAATGAACTCATTGCTCTCATGGAGAGTGGTCTTGGACTAGAACGTGCAC
||  | |  |      ||  | |  || | |||    ||  ||  | |   ||  |   | |      || || | | |||       ||| | || |   |  | || |  |  |   ||||| |||||| ||||||||||||| ||||||||||| || ||||| |||||||||||| | ||  | || ||||||||||| ||||| || |||||||| |
gtgaatacctgatcttactgagcacaaaagtttccccttacaggttttagatttcaattgtgtatgctttatagcccaatgtatctcatttatttcctggttaatcttttggtgcttaatagGTGGATGACCTGGAAGAAGTCAGCGAGTACTACCAGAACAGAGGGTGCTTCAATGAATTAATCTCACTTATGGAGAGTGGACTTGGGCTTGAACGTGCTC

upper sequence: GRMZM2G325285_T01 (Zea mays), 3'ss of exon 14
lower sequence: AT3G11130.1 (Arabidopsis thaliana), 3'ss of exon 24
gtatacaagtaggagcacatacttaataatttttttgtagtatctgctttatagcagagcttctatcactatgatctatttttttctcatatctgcttttgtatttttgtttagGTTGATGACTTGGAAGAAGTCAGTGAGTACTACCAAAATAGAGGATGCTTCAATGAACTCATTGCTCTCATGGAGAGTGGTCTTGGACTAGAACGTGCAC
||  | || ||  ||  | || ||    |         ||| | |   |||||   | | ||| ||  | ||  | |||   ||| |   |  |  ||||||  |||  |  |||| |||||| |||||||||| || ||||||||||| || |||||||||||||||||| | ||  | || ||||||||||| ||||| || |||||||| |
gtggataaataacagatcctagttcccgag------aaagttttttagttataattgggtttcaatttcaattttgtatgcctttttgtaa--tatttttgtgctttaat--agGTGGATGACCTGGAAGAAGTAAGCGAGTACTACCAGAACAGAGGATGCTTCAATGAATTGATCTCCCTTATGGAGAGTGGACTTGGTCTGGAACGTGCTC

upper sequence: GRMZM2G325285_T01 (Zea mays), 3'ss of exon 14
lower sequence: Vv06s0004g06860.t01 (Vitis vinifera), 3'ss of exon 24
gtatacaagtaggagcacatacttaataatttttttgtagtatctgctttatagcagagcttctatcactatgatctatttttttctcatatctgcttttgtatttttgtttagGTTGATGACTTGGAAGAAGTCAGTGAGTACTACCAAAATAGAGGATGCTTCAATGAACTCATTGCTCTCATGGAGAGTGGTCTTGGACTAGAACGTGCAC
  || ||  |||     ||   || ||||  |   | |  ||     |||| |       | |||   || |  |  | |  | | | || |  | | || |||  ||   ||||| ||||| ||||||||||||||||| || ||||| || || |||||||| ||||| |||||  ||||||||||||||||  | ||| | ||||||||||
-aatgcagctagctattca---tttataacctcagtatgttactctatttagaa------tcctagtcctgt--ttgaatcctctttgatcttggatattttatgatt--ctagGTGGATGATTTGGAAGAAGTCAGTGACTATTACCAGAACAGGGGATGCTTTAATGAGCTCATATCTCTCATGGAGAGTGGATTGGGATTGGAACGTGCAC

upper sequence: GRMZM2G325285_T01 (Zea mays), 3'ss of exon 14
lower sequence: Vv13s0067g01290.t01 (Vitis vinifera), 3'ss of exon 24
---------------------gtatacaagtaggagcacatacttaata---atttttttgtagtatctgctttatagcagagcttctatcactatgat-----ctatttttttctcatatctgcttt-----tgtatt--tttg-----tttagGTTGATGACTTGGAAGAAGTCAGTGAGTACTACCAAAATAGAGGATGCTTCAATGAACTCATTGCTCTCATGGAGAGTGGTCTTGGACTAGAACGTGCAC
                     |||     | | ||  ||||  | || |   ||| || | |   |  | | || |    ||||||| |   |||   |     || |||| || |||  |||  |||     ||||||  ||||     | ||||| ||||| ||||| || |||||||| || ||||| |||||||||||||||||||| || ||  | ||||||||||||||||| ||  | || |||||||
gtaatgtattgttttttaagggtagggtgggatgataacatcataaaaatggattgttgtttcaaaatttccttctgtatgagcttccaagcctaatgttttcgcttttttattatcaggtctaatttcctagtgtattgatttgaattttgtagGTCGATGATTTGGAGGAGGTCAGTGATTATTACCAGAATAGAGGATGCTTCAATGAGCTAATATCACTCATGGAGAGTGGTCTGGGCTTGGAGCGTGCAC

upper sequence: GRMZM2G325285_T01 (Zea mays), 3'ss of exon 14
lower sequence: EFJ24508 (Selaginella moellendorffii), 3'ss of exon 24
gtatacaagtaggagcacatacttaataatttttttgtagtatctgctttatagcagagcttctatcactatgatctatttttttctcatatctgcttttgtatttttgtttagGTTGATGACTTGGAAGAAGTCAGTGAGTACTACCAAAATAGAGGATGCTTCAATGAACTCATTGCTCTCATGGAGAGTGGTCTTGGACTAGAACGTGCAC
                                                | |    | || ||||     |||  ||||| |||   |  | |     | |||  ||   |  |||| ||||| ||||| ||||| ||||| |||||||| ||||| ||| | ||| ||||||| ||| |||| ||||| |||||||||||||| || || ||||
-----------------------------------------------gtaaggctatagtttctg--gttatactctatctttggttggtcta---atctgttattaaatccagGTGGATGATTTGGAGGAAGTGAGTGACTACTACCAGAATAGGGGACGATTCGATGAACTGATTTCTCTAATGGAAAGTGGTCTTGGACTCGACCGCGCAC

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: 519

GGCTAACAGTGCCAAAACATGGAAGGAGGTCTGCTTTGCTTGTGTTGACGCCGAGGAGTTCCGTCTTGCACAAATTTGTGGTCTCAATATTATTATTCAGgtatacaagt ... ttttgtttagGTTGATGACTTGGAAGAAGTCAGTGAGTACTACCAAAATAGAGGATGCTTCAATGAACTCATTGCTCTCATGGAGAGTGGTCTTGGACTAGAACGTGCAC


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 326

GGCTAACAGTGCCAAAACATGGAAGGAGGTCTGCTTTGCTTGTGTTGACGCCGAGGAGTTCCGTCTTGCACAAATTTGTGGTCTCAATATTATTATTCAGgtatacaagt ... ttttgtttagGTTGATGACTTGGAAGAAGTCAGTGAGTACTACCAAAATAGAGGATGCTTCAATGAACTCATTGCTCTCATGGAGAGTGGTCTTGGACTAGAACGTGCAC


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 372

GGCTAACAGTGCCAAAACATGGAAGGAGGTCTGCTTTGCTTGTGTTGACGCCGAGGAGTTCCGTCTTGCACAAATTTGTGGTCTCAATATTATTATTCAGgtatacaagt ... ttttgtttagGTTGATGACTTGGAAGAAGTCAGTGAGTACTACCAAAATAGAGGATGCTTCAATGAACTCATTGCTCTCATGGAGAGTGGTCTTGGACTAGAACGTGCAC


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 628

GGCTAACAGTGCCAAAACATGGAAGGAGGTCTGCTTTGCTTGTGTTGACGCCGAGGAGTTCCGTCTTGCACAAATTTGTGGTCTCAATATTATTATTCAGgtatacaagt ... ttttgtttagGTTGATGACTTGGAAGAAGTCAGTGAGTACTACCAAAATAGAGGATGCTTCAATGAACTCATTGCTCTCATGGAGAGTGGTCTTGGACTAGAACGTGCAC




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cttctatcactatgatctatttttttctcatatctgcttttgtatttttgtttagGTTGATGACTTGGAAGAAGTCAGTGAGTACTACCAAAATAGAGGATGCTTCAATGAACTCATTGCTCTCATGGAGAGTGGTCTTGGACTAGAACGTGCAC
                                            tttttgttt  CT-rich tract
                                     ttttgtatttttgttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatacaagtaggagcacatacttaataatttttttgtagtatctgctttatagcagagcttctatcactatgatctatttttttctcatatctgcttttgtatttttgtttagGTTGATGACTTGGAAGAAGTCAGTGAGTACTACCAAAATAGAGGATGCTTCAATGAACTCATTGCTCTCATGGAGAGTGGTCTTGGACTAGAACGTGCAC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGA