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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatacaagtaggagcacatacttgataattttttctagtctgttttataacagagcttctatgatctatttctgtctgacatgtctgattttgtatttttgtttagGTTGATGACTTGGAAGAAGTCAGTGAGTACTACCAGAATAGAGGATGCTTCAGTGAACTTATTGCTCTCATGGAGAGTGGTCTTGGACTTGAACGTGCAC

Basic information

species Zea mays
transcript GRMZM5G804382_T01
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM5G804382_T01 (Zea mays), 3'ss of exon 1
lower sequence: LOC_Os11g01380.1 (Oryza sativa), 3'ss of exon 24
gtatacaagtaggagcacatacttgataattttttctagtctgttttataacagagcttctatgatctat-ttctgtctgacatgtctgattttgtatttttgtttagGTTGATGACTTGGAAGAAGTCAGTGAGTACTACCAGAATAGAGGATGCTTCAGTGAACTTATTGCTCTCATGGAGAGTGGTCTTGGACTTGAACGTGCAC
||||| |   |||||||   || || ||    |    |   | ||| |  |||   ||| | | |||||  || | ||| |||    |          |||||| ||||||||||| ||||| ||||| ||||| ||||||||||| |||||||| |||| |||||||||| | |||||||| |||||||| ||||| || ||||| |
gtatatatacaggagca---acctgttagaactaa--aacatatttcagtacaagtcttttcttatctagattttttctaacaccctt----------ttttgtatagGTTGATGATTTGGAGGAAGTAAGTGAATACTACCAGAACAGAGGATGTTTCAATGAACTTATTTCCCTCATGGAAAGTGGTCTAGGACTGGAGCGTGCTC

upper sequence: GRMZM5G804382_T01 (Zea mays), 3'ss of exon 1
lower sequence: LOC_Os12g01390.1 (Oryza sativa), 3'ss of exon 24
gtatacaagtaggagcacatacttgataattttttctagtctgttttataacagagcttctatgatctat-ttctgtctgacatgtctgattttgtatttttgtttagGTTGATGACTTGGAAGAAGTCAGTGAGTACTACCAGAATAGAGGATGCTTCAGTGAACTTATTGCTCTCATGGAGAGTGGTCTTGGACTTGAACGTGCAC
||||| |   |||| ||   || || ||    |    |   | ||| |  |||   ||| | | |||||  || | ||| |||    |  ||||||||        |||||||||| ||||| ||||| ||||| ||||||||||| |||||||| |||| |||||||||| | |||||||| |||||||| ||||| || ||||| |
gtatatatacaggacca---acctgttagaactaa--aacatatttcagtacaagtcttttcttatctagattttttctaacacccttttttttgtat--------agGTTGATGATTTGGAGGAAGTAAGTGAATACTACCAGAACAGAGGATGTTTCAATGAACTTATTTCCCTCATGGAAAGTGGTCTAGGACTGGAGCGTGCTC

upper sequence: GRMZM5G804382_T01 (Zea mays), 3'ss of exon 1
lower sequence: GLYMA02G39360.1 (Glycine max), 3'ss of exon 24
gtatacaagtaggagcacatacttgataattttttctagtctgttttataacagagcttctatgatctatttctgtctgacatgtctgattttgtatttttgtttagGTTGATGACTTGGAAGAAGTCAGTGAGTACTACCAGAATAGAGGATGCTTCAGTGAACTTATTGCTCTCATGGAGAGTGGTCTTGGACTTGAACGTGCAC
    |   | |   | | |   |||  ||    |   ||   |     | |       | | | || |  |  ||| |||    |     | | |||| || |  |||| ||||| |||||||| || |||||||  |||||||| ||||||||||| | |||||| ||  |||| ||||||||||| |||||||| || ||||| |
----attgggaaatgtagaacattggcaacaagtggcagatagacagttgattag---tttgttattttctgttgtttgattactaattctctttattattatgaagGTGGATGATTTGGAAGAGGTTAGTGAGTTTTACCAGAACAGAGGATGCTTTAATGAACTGATATCTCTAATGGAGAGTGGACTTGGACTGGAGCGTGCCC

upper sequence: GRMZM5G804382_T01 (Zea mays), 3'ss of exon 1
lower sequence: GLYMA18G02960.1 (Glycine max), 3'ss of exon 23
-gtatacaagtaggagcacatacttgataattttttctagtctgttttataacagagcttctatgatctatttctgtctgacatgtctgattttgtatttttgtttagGTTGATGACTTGGAAGAAGTCAGTGAGTACTACCAGAATAGAGGATGCTTCAGTGAACTTATTGCTCTCATGGAGAGTGGTCTTGGACTTGAACGTGCAC
 |   | ||  |          | | |      | |  ||| ||||   | | ||   ||| |     ||||      || ||  | | ||| || ||||     ||||| |||||||||||||| |||||||| || ||||| |||||||| ||||||| ||| || ||  | || |||||||||||| | ||| | ||||| ||||
agagaaaaaaaaatgctgtgagcattacttaaatctgcagtttgttaccttatagtctttccaatgcttatta-----tgtcaattttcattgtgaatttg---gtagGTGGATGACTTGGAAGAGGTCAGTGAATATTACCAAAATAGAGGTTGCTTCAATGAGCTAATATCGCTTATGGAGAGTGGTTTAGGATTAGAACGGGCAC

upper sequence: GRMZM5G804382_T01 (Zea mays), 3'ss of exon 1
lower sequence: GLYMA01G38580.1 (Glycine max), 3'ss of exon 24
-----gtatacaagtaggagcacatacttgataattttttctagtctgttttataacagagcttctatgatctatttctgtctgacatgtctgat-tttgtatttttgtttagGTTGATGACTTGGAAGAAGTCAGTGAGTACTACCAGAATAGAGGATGCTTCAGTGAACTTATTGCTCTCATGGAGAGTGGTCTTGGACTTGAACGTGCAC
     | | |  | ||  | ||  |    || ||  ||||   |  || ||| |  |  | |||   ||| ||     ||||||| ||   |  | | ||| || |  |  |||| ||||| ||||| || || || |||||||| ||||| ||||||||||||| |||||| ||  |||| |||||||||||  | ||| | || |||||||
tagtagcaaaatactaaaaacaagtgacagaaaaactttt---gattgctttgt--ctaaccttt--tgacct-----tgtctga-atacttactatctgttttatattgaagGTGGATGATTTGGAGGAGGTTAGCGAGTACTATCAGAACAGAGGATGCTTCAATGAACTCATATCTCTAATGGAGAGTGGGTTAGGATTGGAGCGTGCAC

upper sequence: GRMZM5G804382_T01 (Zea mays), 3'ss of exon 1
lower sequence: GLYMA14G37510.1 (Glycine max), 3'ss of exon 22
gtatacaagtaggagcacatacttgataattttttctagtctgttttataacagagcttctatgatctatttctgtctgacatgtctgattttgtatttttgtttagGTTGATGACTTGGAAGAAGTCAGTGAGTACTACCAGAATAGAGGATGCTTCAGTGAACTTATTGCTCTCATGGAGAGTGGTCTTGGACTTGAACGTGCAC
    |   | |   | | |   |||  ||    | | ||   |  |  | |       | | | || |  |  ||| ||||   |     | | |||| || |  |||| ||||| |||||||| || |||||||  || ||||| ||||||||||| | |||||| ||  |||| ||||||||||| |||||||| || ||||| |
----attgggaaatgtagaacattggcaacaagtgccagatagactgttgattag---tttgttattttctgttgtttgactgctaattctctttattattatgaagGTGGATGATTTGGAAGAGGTTAGTGAGTTTTATCAGAACAGAGGATGCTTTAATGAACTCATATCTCTAATGGAGAGTGGACTTGGACTGGAGCGTGCCC

upper sequence: GRMZM5G804382_T01 (Zea mays), 3'ss of exon 1
lower sequence: GLYMA11G35460.1 (Glycine max), 3'ss of exon 23
gtatacaagtaggagcacatacttgataattttttctagtctgttttataacagagcttctatgatctatttc-tgtctgacatgtctgattt---tgtatttttgtttagGTTGATGACTTGGAAGAAGTCAGTGAGTACTACCAGAATAGAGGATGCTTCAGTGAACTTATTGCTCTCATGGAGAGTGGTCTTGGACTTGAACGTGCAC
       || || |  | || ||       ||  |  | ||||   | |           |||  ||| |    ||  |   |||||   |||   |||   |||| | |||| |||||||||||||| |||||||| || ||||| |||||||| ||||||| ||| || ||  | ||||||||||||||| | ||| | ||||| ||||
-------aggagaaaaaaatgctgtgagcattacttgaatctgcagtttgttta---ccttatagtctttccaatgcttattatgtcaattttcattgtgaatttggt-agGTGGATGACTTGGAAGAGGTCAGTGAATATTACCAAAATAGAGGTTGCTTCAATGAGCTAATATCCCTCATGGAGAGTGGTTTAGGATTAGAACGGGCAC

upper sequence: GRMZM5G804382_T01 (Zea mays), 3'ss of exon 1
lower sequence: GLYMA02G42560.1 (Glycine max), 3'ss of exon 24
gtatacaagtaggagcacatacttgataattttttctagt-ctgtttta-taacagagcttctat-gatctatttctgtctgacatgtctgattttgtatttttgttta-gGTTGATGACTTGGAAGAAGTCAGTGAGTACTACCAGAATAGAGGATGCTTCAGTGAACTTATTGCTCTCATGGAGAGTGGTCTTGGACTTGAACGTGCAC
           ||      | |||| || ||     || | ||| | |  |   || | |  ||| ||  |  |  ||  |     |||   ||||  |||  | || | ||| ||||||||||||||||||||||| || ||||| |||||||| ||||||| ||| || ||  |||| |||||||||||| | ||  | ||||| ||||
-----------gggtgttttgcttggtatttgaacttaatgctgatctgctggtagtgatcttattgaatttctaatgcttattgcgtcatttttttaattaattttaaagGTGGATGACTTGGAAGAAGTCAGTGAATATTACCAAAATAGAGGTTGCTTCAATGAGCTAATATCTCTGATGGAGAGTGGTTTAGGGTTAGAACGGGCAC

upper sequence: GRMZM5G804382_T01 (Zea mays), 3'ss of exon 1
lower sequence: GLYMA14G06340.1 (Glycine max), 3'ss of exon 24
gtatacaagtaggagcacatacttgataattttttctagtct--gttttataacagagcttctat-gatctatttctgtctgacatgtctgattttgtatttttgtt-tagGTTGATGACTTGGAAGAAGTCAGTGAGTACTACCAGAATAGAGGATGCTTCAGTGAACTTATTGCTCTCATGGAGAGTGGTCTTGGACTTGAACGTGCAC
           ||      | |||| ||  |     || | |   |||  ||  || | |  ||| ||  |  |  ||  |     |||   |||| ||||  | |  ||||| ||||||||||||||||||||||| || ||||| || ||||| ||||||| ||| || ||  ||||||||||||||||| | ||  | ||||| ||||
-----------gggtgttgtgcttgttatatgaacttaatgttgatttgctactagtgatcttattgaatttctaatgcttattgcgtcattttttttattaatttcatagGTGGATGACTTGGAAGAAGTCAGTGAATATTACCAAAACAGAGGTTGCTTCAATGAGCTCATATCTCTCATGGAGAGTGGTTTAGGGTTAGAACGGGCAC

upper sequence: GRMZM5G804382_T01 (Zea mays), 3'ss of exon 1
lower sequence: AT3G08530.1 (Arabidopsis thaliana), 3'ss of exon 24
---------------------gtatacaagtaggagc--acatacttgataattttttctagtctgttttataacagagcttctatgatctatttctgtctgacatgtctgattttgtatttttgtttagGTTGATGACTTGGAAGAAGTCAGTGAGTACTACCAGAATAGAGGATGCTTCAGTGAACTTATTGCTCTCATGGAGAGTGGTCTTGGACTTGAACGTGCAC
                     | | | ||||     |  |||   || | | ||   |   || || |||||| |  |   | | | || ||||||         ||  | || || |  |  |   ||||| |||||| ||||||||||||| |||||||||||||| ||||| ||||||| |||| | ||  | || ||||||||||| ||||| ||||||||||| |
gtgaatacctgatcttactgagcacaaaagtttccccttacaggttttagatttcaattgtgtatgctttatagcccaatgtatctcatttatttcc--------tggttaatcttttggtgcttaatagGTGGATGACCTGGAAGAAGTCAGCGAGTACTACCAGAACAGAGGGTGCTTCAATGAATTAATCTCACTTATGGAGAGTGGACTTGGGCTTGAACGTGCTC

upper sequence: GRMZM5G804382_T01 (Zea mays), 3'ss of exon 1
lower sequence: AT3G11130.1 (Arabidopsis thaliana), 3'ss of exon 24
gtatacaagtaggagcacatactt---gataattttttctagtctgttttataacagagcttctatgatctatttctgtctgacatgtctgattttgtatttttgtttagGTTGATGACTTGGAAGAAGTCAGTGAGTACTACCAGAATAGAGGATGCTTCAGTGAACTTATTGCTCTCATGGAGAGTGGTCTTGGACTTGAACGTGCAC
||  | || ||  ||  | || ||   || ||  |||| ||||     ||       |  ||| ||  | |||  || | ||  || |    ||||||  |||  |  |||| |||||| |||||||||| || |||||||||||||| ||||||||||||| |||| | ||  | || ||||||||||| ||||| || |||||||| |
gtggataaataacagatcctagttcccgagaaagttttttagttataattgggtttcaatttcaattttgtatgcctttttgtaatat----ttttgtgctttaat--agGTGGATGACCTGGAAGAAGTAAGCGAGTACTACCAGAACAGAGGATGCTTCAATGAATTGATCTCCCTTATGGAGAGTGGACTTGGTCTGGAACGTGCTC

upper sequence: GRMZM5G804382_T01 (Zea mays), 3'ss of exon 1
lower sequence: Vv06s0004g06860.t01 (Vitis vinifera), 3'ss of exon 24
gtatacaagtaggagcacatacttgataattttttctagtctgttttataacagagcttctatgatctatttctgtctgacatgtctgattttgtatttttgtttagGTTGATGACTTGGAAGAAGTCAGTGAGTACTACCAGAATAGAGGATGCTTCAGTGAACTTATTGCTCTCATGGAGAGTGGTCTTGGACTTGAACGTGCAC
  || ||  |||     |||   | |      | | |       |||| ||      | || |  |  | | || | |||  | |  ||| || |||  ||   ||||| ||||| ||||||||||||||||| || |||||||| || |||||||| | ||| || ||  ||||||||||||||||  | ||| | ||||||||||
-aatgcagctagctattcatttataacctcagtatgttactctatttagaatcctagtcctgt--ttgaatcctctttga--tcttggatattttatgatt--ctagGTGGATGATTTGGAAGAAGTCAGTGACTATTACCAGAACAGGGGATGCTTTAATGAGCTCATATCTCTCATGGAGAGTGGATTGGGATTGGAACGTGCAC

upper sequence: GRMZM5G804382_T01 (Zea mays), 3'ss of exon 1
lower sequence: Vv13s0067g01290.t01 (Vitis vinifera), 3'ss of exon 24
--------------------------gtatacaagtaggagcacatacttg-ataattttttctagtctgttttataacagagcttctatgatctat---------ttctgtctgacatgtctgattt-----tgtatt--tttg-----tttagGTTGATGACTTGGAAGAAGTCAGTGAGTACTACCAGAATAGAGGATGCTTCAGTGAACTTATTGCTCTCATGGAGAGTGGTCTTGGACTTGAACGTGCAC
                          ||       ||  | || | |  || ||  || |||| |   |   || |    ||||||| | |    ||         || |   |  || |||| ||||     ||||||  ||||     | ||||| ||||| ||||| || |||||||| || |||||||||||||||||||||| ||| || ||  | ||||||||||||||||| ||  | || |||||||
gtaatgtattgttttttaagggtagggtgggatgataacatcataaaaatggattgttgtttcaaaatttccttctgtatgagcttccaagcctaatgttttcgcttttttattatcaggtctaatttcctagtgtattgatttgaattttgtagGTCGATGATTTGGAGGAGGTCAGTGATTATTACCAGAATAGAGGATGCTTCAATGAGCTAATATCACTCATGGAGAGTGGTCTGGGCTTGGAGCGTGCAC

upper sequence: GRMZM5G804382_T01 (Zea mays), 3'ss of exon 1
lower sequence: EFJ24508 (Selaginella moellendorffii), 3'ss of exon 24
gtatacaagtaggagcacatacttgataattttttctagtctgttttataacagagcttctatgatctatttctgtctgacatgtctgattttgtatttttgtttagGTTGATGACTTGGAAGAAGTCAGTGAGTACTACCAGAATAGAGGATGCTTCAGTGAACTTATTGCTCTCATGGAGAGTGGTCTTGGACTTGAACGTGCAC
                                             | |    | || ||||        | | | | ||    |||| || |  ||||    |  |||| ||||| ||||| ||||| ||||| |||||||||||||| ||| | |||  |||||| ||| |||| ||||| |||||||||||||| || || ||||
--------------------------------------------gtaaggctatagtttctggttatactctatctttggttggtctaatctgttattaa-atccagGTGGATGATTTGGAGGAAGTGAGTGACTACTACCAGAATAGGGGACGATTCGATGAACTGATTTCTCTAATGGAAAGTGGTCTTGGACTCGACCGCGCAC

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|211133343|gb|FL220151.1|FL220151
EST:     CAATATTATTATTCAG                         GTTGATGACTTGGAAGAAGTCAGTGAGTACTACCAGAATAGAGGATGCTTC
genomic: CAATATTATTATTCAGgtatacaagt ... ttttgtttagGTTGATGACTTGGAAGAAGTCAGTGAGTACTACCAGAATAGAGGATGCTTC
EST: gi|211133340|gb|FL220148.1|FL220148
EST:     CAATATTATTATTCAG                         GTTGATGACTTGGAAGAAGTCAGTGAGTACTACCAGAATAGAGGATGCTTC
genomic: CAATATTATTATTCAGgtatacaagt ... ttttgtttagGTTGATGACTTGGAAGAAGTCAGTGAGTACTACCAGAATAGAGGATGCTTC

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: 225

CAATATTATTATTCAGgtatacaagt ... ttttgtttagGTTGATGACTTGGAAGAAGTCAGTGAGTACTACCAGAATAGAGGATGCTTCAGTGAACTTATTGCTCTCATGGAGAGTGGTCTTGGACTTGAACGTGCAC


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 199

CAATATTATTATTCAGgtatacaagt ... ttttgtttagGTTGATGACTTGGAAGAAGTCAGTGAGTACTACCAGAATAGAGGATGCTTCAGTGAACTTATTGCTCTCATGGAGAGTGGTCTTGGACTTGAACGTGCAC


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 294

CAATATTATTATTCAGgtatacaagt ... ttttgtttagGTTGATGACTTGGAAGAAGTCAGTGAGTACTACCAGAATAGAGGATGCTTCAGTGAACTTATTGCTCTCATGGAGAGTGGTCTTGGACTTGAACGTGCAC


Block sizes: 48 (upstream exon), 48 (downstream exon)
Score: 214

CAATATTATTATTCAGgtatacaagt ... ttttgtttagGTTGATGACTTGGAAGAAGTCAGTGAGTACTACCAGAATAGAGGATGCTTCAGTGAACTTATTGCTCTCATGGAGAGTGGTCTTGGACTTGAACGTGCAC




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

agagcttctatgatctatttctgtctgacatgtctgattttgtatttttgtttagGTTGATGACTTGGAAGAAGTCAGTGAGTACTACCAGAATAGAGGATGCTTCAGTGAACTTATTGCTCTCATGGAGAGTGGTCTTGGACTTGAACGTGCAC
                                            tttttgttt  CT-rich tract
                                    attttgtatttttgtt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatacaagtaggagcacatacttgataattttttctagtctgttttataacagagcttctatgatctatttctgtctgacatgtctgattttgtatttttgtttagGTTGATGACTTGGAAGAAGTCAGTGAGTACTACCAGAATAGAGGATGCTTCAGTGAACTTATTGCTCTCATGGAGAGTGGTCTTGGACTTGAACGTGCAC

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