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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatgtatctagcttattccttagcgattggagcattaacttctctttaggattcaccttttattccttaagcaaataatcgtgtatcatatgagggtgcattgttgctctgctatatttatttgtgtagcttagacgggctttgaatagtatcatggaaatgttgaatcttaagcaaatcattgtgctttctgctgtagGGTCTCTTCCTCTCCCATGGGCAATCAGAATGAAGGTTGCACTCGGAGCAGCAAAGGGTCTGGCTTTCCTTCATGAAGAAGCAGAAAGACCAGTCATTTA

Basic information

species Zea mays
transcript GRMZM2G132184_T02
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G132184_T03 (Zea mays), 3'ss of exon 3
lower sequence: LOC_Os09g19700.1 (Oryza sativa), 3'ss of exon 3
gtatgtatctagcttattcctta-gcgattggagcattaacttctctttaggattcaccttttattccttaagcaaataatcgtgtatcatatgagggtgcattgttgctctgctatatttatttgtgtagcttagacgggctttgaatagtatcatggaaatgttgaatcttaagcaaatcattgtgctttctgctgtagGGTCTCTTCCTCTCCCATGGGCAATCAGAATGAAGGTTGCACTCGGAGCAGCAAAGGGTCTGGCTTTCCTTCATGAAGAAGCAGAAAGACCAGTCATTTA
||| || |||  |   || || | |  |||| | | | || || | |  |          |||| |   | | |  || ||    |||  |  |  | |    ||  |   |     |||   |  ||  |||   |      || |||||    || ||||| ||||||||||    | | ||  |    ||  || ||||||||||||||||||| ||| | ||||||||||||||||| || ||||||||||||||||| |||||||||||||||||||||||||||||||| |||||
gtacgtgtctgaccagtttctcaagacattgaaacttcaatttgtatacaatgcctgtgctttaatgaatgaacttatcatt-catatt-tgagtagctcttctgaagtgtttggtcattgcatcttgctgctggaaaaaatattaaatag----atagaaatattgaatcttatatgatttatgat----tcacctatagGGTCTCTTCCTCTCCCTTGGTCCATCAGAATGAAGGTTGCTCTTGGAGCAGCAAAGGGTCTTGCTTTCCTTCATGAAGAAGCAGAAAGACCAGTTATTTA

upper sequence: GRMZM2G132184_T03 (Zea mays), 3'ss of exon 3
lower sequence: GLYMA01G04930.1 (Glycine max), 3'ss of exon 3
gtatgtatctagcttattccttagcgattggagcattaacttctctttaggattcaccttttattccttaagcaaataatcgtgtatcatatgagggtgcattgttgctctgctatatttatttgtgtagcttagacgggctttgaatagtatcatggaaatgttgaatcttaagcaaatcattgtgctttctgctgtagGGTCTCTTCCTCTCCCATGGGCAATCAGAATGAAGGTTGCACTCGGAGCAGCAAAGGGTCTGGCTTTCCTTCATGAAGAAGCAGAAAGACCAGTCATTTA
                                                                              ||| |   |   |  ||    ||    |  |  ||| ||| | ||| |||         ||  ||||  |  | |  |    |||||   || |  | |||| | |||            ||| ||  | ||||| |||||| | || ||||||||  ||||||| ||||| || |||||||| ||||| |||||||||||||| ||| ||||||| || ||
---------------------------------------------------------------------------tctatcattggtagaacaagaactcaaaactatt--gctgtatatttttatgtt-------tggattttg--tccttttttatttatgttc--tcatgtggaaattaatgt------------agGATCCATGCCTCTTCCATGGTCCATTAGAATGAAAATTGCACTAGGAGCTGCTAAGGGTCTTGCTTTTCTTCATGAAGAAGCTGAACGACCAGTAATATA

upper sequence: GRMZM2G132184_T03 (Zea mays), 3'ss of exon 3
lower sequence: GLYMA08G40770.1 (Glycine max), 3'ss of exon 3
gtatgtatctagcttattccttagcgattggagcattaacttctctttaggattcaccttttattccttaagcaaataatcgtgtatcatatgagggtgcattgttgctctgctatatttatttgtgtagcttagacgggctttgaatagtatcatggaaatgttgaatcttaagcaaatcattgtgctttctgctgtagGGTCTCTTCCTCTCCCATGGGCAATCAGAATGAAGGTTGCACTCGGAGCAGCAAAGGGTCTGGCTTTCCTTCATGAAGAAGCAGAAAGACCAGTCATTTA
                                                                                            | || || ||| | | |  |   |    | || ||    |       | ||||| ||    |||     |||    ||| | | |||  ||| |   || |   |||||||| || ||||| |||||| | || || |||||  ||||||| ||||| ||||||||||| ||||| |||||||| ||||| ||| ||||||| || ||
--------------------------------------------------------------------------------------------gtggatggattatggattggaacttcaaacttctgcttatactctttgttttgattatatccat-----tgtatgttctcatgtaaaagattatatgtttt---gtagGGTCCCTGCCTCTTCCATGGTCCATTAGGATGAAAATTGCACTTGGAGCTGCAAAGGGTCTTGCTTTTCTTCATGAGGAAGCTGAACGACCAGTAATATA

upper sequence: GRMZM2G132184_T03 (Zea mays), 3'ss of exon 3
lower sequence: GLYMA02G02570.1 (Glycine max), 3'ss of exon 3
gtatgtatctagcttattccttagcgattggagcattaacttctctttaggattcaccttttattccttaagcaaataatcgtgtatcatatgagggtgcattgttgctctgctatatttatttgtgtagcttagacgggctttgaatagtatcatggaaatgttgaatcttaagcaaatcattgtgctttctgctgtagGGTCTCTTCCTCTCCCATGGGCAATCAGAATGAAGGTTGCACTCGGAGCAGCAAAGGGTCTGGCTTTCCTTCATGAAGAAGCAGAAAGACCAGTCATTTA
                                                                                        || |  ||  | | ||   |||    | |  ||||  ||||  ||  | |   |||| ||  | ||       | || | |  |   |   |||| |||     |  |||||| ||  ||||||| |||||| | || ||||||||  ||||||| ||||| || |||||||| ||||| |||||||||||||| ||| ||||||| || ||
------------------------------------------------------------------------------------ctctatcttgggtagaactggaactc----aaaactattgctgtatattttatg---tttgtattttgtccc-----tttttatttatgttc---tcat-gtggaaattaatgtagGATCCATTCCTCTTCCATGGTCCATTAGAATGAAAATTGCACTAGGAGCTGCTAAGGGTCTTGCTTTTCTTCATGAAGAAGCTGAACGACCAGTAATATA

upper sequence: GRMZM2G132184_T03 (Zea mays), 3'ss of exon 3
lower sequence: GLYMA18G16300.1 (Glycine max), 3'ss of exon 4
gtatgtatctagcttattccttagcgattggagcattaacttctctttaggattcaccttttattccttaagcaaataatcgtgtatcatatgagggtgcattgttgctctgctatatttatttgtgtagcttagacgggctttgaatagtatcatggaaatgttgaatcttaagcaaatcattgtgctttctgctgtagGGTCTCTTCCTCTCCCATGGGCAATCAGAATGAAGGTTGCACTCGGAGCAGCAAAGGGTCTGGCTTTCCTTCATGAAGAAGCAGAAAGACCAGTCATTTA
                                                                                          | |||  || ||||   ||     |  | |  || |     ||      | | ||| ||    |||     |||    ||| | | | |  ||| |  | | |  ||||||||| || ||||| |||||| | || || |||||  ||||||| ||||| ||||||||||| ||||| ||||| || ||||| ||| ||||||| || ||
---------------------------------------------------------------------------------------tgaaagagaatggattggaacttcaa-acttctgcttatactcttt------gttgtgattatatccat-----tgtatgttctcatgtacaaaattata-tatgttttgtagGGTCCCTACCTCTTCCATGGTCCATTAGGATGAAAATTGCACTAGGAGCTGCAAAGGGTCTTGCTTTTCTTCACGAGGAAGCTGAACGACCAGTAATATA

upper sequence: GRMZM2G132184_T03 (Zea mays), 3'ss of exon 3
lower sequence: Vv01s0026g01620.t01 (Vitis vinifera), 3'ss of exon 3
gtatgtatctagcttattccttagcgattggagcattaacttctctttaggattcaccttttattccttaagcaaataatcgtgtatcatatgagggtgcattgttgctctgctatatttatttgtgtagcttagacgggctttgaat-agtatcatggaaatgttgaatcttaagcaaatcattgtgctttctgctgtagGGTCTCTTCCTCTCCCATGGGCAATCAGAATGAAGGTTGCACTCGGAGCAGCAAAGGGTCTGGCTTTCCTTCATGAAGAAGCAGAAAGACCAGTCATTTA
                                                                                                    || |||     |  ||| | | |        || ||       |   | |||   ||   |||  | ||| ||   |  || ||     |||    ||||||| | || ||||| |||||||| || || |||||  ||||||| || || || |||||||| || || |||||||| ||||||||||| ||||| || ||
----------------------------------------------------------------------------------------------------atggtttactagagatactgactccctgctttttgataaatgatttgtgagtgcaatatcaattattaatgtttt-ctcatgataacaattttatatgtagGGGCCCTGCCTCTTCCATGGGCCATAAGGATGAAAATTGCACTAGGTGCTGCTAAGGGTCTTGCATTTCTTCATGAGGAAGCAGAAAGGCCAGTTATATA

upper sequence: GRMZM2G132184_T03 (Zea mays), 3'ss of exon 3
lower sequence: Vv14s0108g00380.t01 (Vitis vinifera), 3'ss of exon 3
gtatgtatctagcttattccttagcgattggagcattaacttctctttaggattcaccttttattccttaagcaaataatcgtgtatcatatgagggtgcattgttgctctgctatatttatttgtgtagcttagacgggc--tttgaatagtatcatggaaatgttgaatctta---agcaaatcattgtgctttctgc-tgtagGGTCTCTTCCTCTCCCATGGGCAATCAGAATGAAGGTTGCACTCGGAGCAGCAAAGGGTCTGGCTTTCCTTCATGAAGAAGCAGAAAGACCAGTCATTTA
                                                                                                        |||         ||  ||||| | |   |     |    ||| | ||   |  |||   | || ||| |||    | |  | || ||| | | ||| || |||| | || ||||| || ||| | |||||||||||  ||||||| || || ||||||||||| || || |||||||| ||||| ||||| ||||| || ||
--------------------------------------------------------------------------------------------------------ttgactgatagcatcaatttgagaattgtgattagaaaatttcattatggt--tggtggtatttaatgttatctggtatttaatggtgttatgtgcctgcagGGGCCCTGCCTCTTCCTTGGTCCATCAGAATGAAAATTGCACTTGGTGCTGCAAAGGGTCTTGCCTTTCTTCATGAGGAAGCTGAAAGGCCAGTAATATA

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|76282950|gb|DV022518.1|DV022518
EST:     GGTCTATGAATTCATGCCTCGTGGCAGTTTGGATAACCATCTTTTTAGAA                         GGTCTCTTCCTCTCCCATGGGCAATCAGAATGAAGGTTGCACTCGGAGCAG
genomic: GGTCTATGAATTCATGCCTCGTGGCAGTTTGGATAACCATCTTTTTAGAAgtatgtatct ... tctgctgtagGGTCTCTTCCTCTCCCATGGGCAATCAGAATGAAGGTTGCACTCGGAGCAG
EST: gi|148928770|gb|EC873531.2|EC873531
EST:     GGTCTATGAATTCATGCCTCGTGGCAGTTTGGATAACCATCTTTTTAGAA                         GGTCTCTTCCTCTCCCATGGGCAATCAGAATGAAGGTTGCACTCGGAGCAG
genomic: GGTCTATGAATTCATGCCTCGTGGCAGTTTGGATAACCATCTTTTTAGAAgtatgtatct ... tctgctgtagGGTCTCTTCCTCTCCCATGGGCAATCAGAATGAAGGTTGCACTCGGAGCAG
EST: gi|5499049|gb|AI854916.1|AI854916
EST:     GGTCTATGAATTCATGCCTCGTGGCAGTTTGGATAACCATCTTTTTAGAA                         GGTCTCTTCCTCTCCCATGGGCAATCAGAATGAAGGTTGCACTCGGAGCAG
genomic: GGTCTATGAATTCATGCCTCGTGGCAGTTTGGATAACCATCTTTTTAGAAgtatgtatct ... tctgctgtagGGTCTCTTCCTCTCCCATGGGCAATCAGAATGAAGGTTGCACTCGGAGCAG

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: 224

AATTTGGTCAGATTGATTGGATATTGTGTTGAAGATGACCAAAGGTTGCTGGTCTATGAATTCATGCCTCGTGGCAGTTTGGATAACCATCTTTTTAGAAgtatgtatct ... tctgctgtagGGTCTCTTCCTCTCCCATGGGCAATCAGAATGAAGGTTGCACTCGGAGCAGCAAAGGGTCTGGCTTTCCTTCATGAAGAAGCAGAAAGACCAGTCATTTA


Block sizes: 47 (upstream exon), 49 (downstream exon)
Score: 141

AATTTGGTCAGATTGATTGGATATTGTGTTGAAGATGACCAAAGGTTGCTGGTCTATGAATTCATGCCTCGTGGCAGTTTGGATAACCATCTTTTTAGAAgtatgtatct ... tctgctgtagGGTCTCTTCCTCTCCCATGGGCAATCAGAATGAAGGTTGCACTCGGAGCAGCAAAGGGTCTGGCTTTCCTTCATGAAGAAGCAGAAAGACCAGTCATTTA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 172

AATTTGGTCAGATTGATTGGATATTGTGTTGAAGATGACCAAAGGTTGCTGGTCTATGAATTCATGCCTCGTGGCAGTTTGGATAACCATCTTTTTAGAAgtatgtatct ... tctgctgtagGGTCTCTTCCTCTCCCATGGGCAATCAGAATGAAGGTTGCACTCGGAGCAGCAAAGGGTCTGGCTTTCCTTCATGAAGAAGCAGAAAGACCAGTCATTTA


Block sizes: 46 (upstream exon), 49 (downstream exon)
Score: 139

AATTTGGTCAGATTGATTGGATATTGTGTTGAAGATGACCAAAGGTTGCTGGTCTATGAATTCATGCCTCGTGGCAGTTTGGATAACCATCTTTTTAGAAgtatgtatct ... tctgctgtagGGTCTCTTCCTCTCCCATGGGCAATCAGAATGAAGGTTGCACTCGGAGCAGCAAAGGGTCTGGCTTTCCTTCATGAAGAAGCAGAAAGACCAGTCATTTA




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aatagtatcatggaaatgttgaatcttaagcaaatcattgtgctttctgctgtagGGTCTCTTCCTCTCCCATGGGCAATCAGAATGAAGGTTGCACTCGGAGCAGCAAAGGGTCTGGCTTTCCTTCATGAAGAAGCAGAAAGACCAGTCATTTA
                                          ctttctgct  CT-rich tract
                     aatcttaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatgtatctagcttattccttagcgattggagcattaacttctctttaggattcaccttttattccttaagcaaataatcgtgtatcatatgagggtgcattgttgctctgctatatttatttgtgtagcttagacgggctttgaatagtatcatggaaatgttgaatcttaagcaaatcattgtgctttctgctgtagGGTCTCTTCCTCTCCCATGGGCAATCAGAATGAAGGTTGCACTCGGAGCAGCAAAGGGTCTGGCTTTCCTTCATGAAGAAGCAGAAAGACCAGTCATTTA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGC