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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagctttctataataggtcaaagatataaagaggacccattagatcagtatggccgtatttcctacccctttgttggcaggcagtacagtatccttttattttctgcagGTGATATCTGGTAAACTATATGCTGGACCTGAAGTTGATGTGTGGAGCTGTGGGGTTATTCTTTATGCTCTTTTATGTGGTACTCTGCCATTTGATGACG

Basic information

species Zea mays
transcript GRMZM2G180704_T01
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G180704_T01 (Zea mays), 3'ss of exon 4
lower sequence: GLYMA13G05700.1 (Glycine max), 3'ss of exon 4
---------------------------gtaagctttctataatag-gtcaaagatataaagaggac-ccattagatcagtatggccgtatttcctacccctttgttggcaggcagtacagtatccttttattttctgcagGTGATATCTGGTAAACTATATGCTGGACCTGAAGTTGATGTGTGGAGCTGTGGGGTTATTCTTTATGCTCTTTTATGTGGTACTCTGCCATTTGATGACG
                            || | | |   || ||  || |    ||| |  |  |   || ||  || |         |||| |  ||   |  ||   |      |   ||  || || ||||   ||||| || ||||| ||| | ||||||||||| ||||| ||||| ||||||||||| || ||| | ||||||||| | ||||| ||||| || |||||||| |
gtttgtaaataattaaattgtaacggaataggatattattattaatgttattattattattattatatcactacttctgagactttacatttacctccttgtgattaataaatca-aggataaactgttgtttttcacagGTTATCTCTGGAAAATTGTATGCTGGACCAGAAGTAGATGTCTGGAGCTGTGGTGTAATTTTATATGCTCTTCTCTGTGGCACTCTTCCTTTTGATGATG

upper sequence: GRMZM2G180704_T01 (Zea mays), 3'ss of exon 4
lower sequence: GLYMA18G49770.1 (Glycine max), 3'ss of exon 5
gtaagctttctataataggtcaaagatataaagaggacccattagatcagtatggccgtatttcctacccctttgttggcaggcagtacagtatccttttattttctgcagGTGATATCTGGTAAACTATATGCTGGACCTGAAGTTGATGTGTGGAGCTGTGGGGTTATTCTTTATGCTCTTTTATGTGGTACTCTGCCATTTGATGACG
               |  || |  || ||| |  | | | |||  ||   |  ||   ||| |  |     | |||     ||    ||       ||| |||||   ||||| || ||||| ||| | ||||||||||||||||| ||||| ||||||||||| || ||| | ||||| ||| | ||||| || || || |||||||| |
--------------gtttgtaatgga-atacacggcaacaatt--attgttgaggatatatatg-tgtgtgtgtgtgtcttggttacac-----tttttcatttttcacagGTTATCTCTGGGAAATTGTATGCTGGACCTGAAGTGGATGTCTGGAGCTGTGGTGTAATTTTATATGCCCTTCTTTGTGGCACCCTTCCTTTTGATGATG

upper sequence: GRMZM2G180704_T01 (Zea mays), 3'ss of exon 4
lower sequence: GLYMA08G26180.1 (Glycine max), 3'ss of exon 4
gtaagctttctataataggtcaaagatataaagaggacccattagatcagtatggccgtatttcctacccctttgttggcaggcagta-cagtatccttttattttctgcagGTGATATCTGGTAAACTATATGCTGGACCTGAAGTTGATGTGTGGAGCTGTGGGGTTATTCTTTATGCTCTTTTATGTGGTACTCTGCCATTTGATGACG
        | | |||| |    || | ||   ||  |   ||| | | || ||     ||| |  |  |   |  ||   |     |      |   ||| |||||   ||||| || ||||| ||||| ||||||||||||||||| ||||| ||||||||||| || ||| | ||||| ||| | ||||| ||||| || |||||||| |
-------gtttgtaatgg----aatacatggcgaaaatt-att-gttgaggatatatatatattgtctcttgtgattcatatttcttggttacactttttcatttttcacagGTTATCTCTGGGAAACTGTATGCTGGACCTGAAGTGGATGTCTGGAGCTGTGGTGTAATTTTATATGCGCTTCTTTGTGGCACTCTTCCTTTTGATGATG

upper sequence: GRMZM2G180704_T01 (Zea mays), 3'ss of exon 4
lower sequence: AT3G01090.2 (Arabidopsis thaliana), 3'ss of exon 4
gtaagctttctataataggtcaaagatataaagaggacccattagatcagtatggccgtatttcctacccctttgttggcaggcagtacagtatccttttattttctgcagGTGATATCTGGTAAACTATATGCTGGACCTGAAGTTGATGTGTGGAGCTGTGGGGTTATTCTTTATGCTCTTTTATGTGGTACTCTGCCATTTGATGACG
|||||   |  |       |||   || | | ||  ||       || | ||  | | | ||||  |      || | |     |||  || |||  |  ||| | | ||||| || || || ||  |||||||||| |||||||| ||||| ||||||||||| || || || || |||||| | ||||| || || ||||||||||| |
gtaagtgcttcagccc---tcaggtatctgaggaatact------ataatta--ggcttgtttcaaa------tgataggttatagtcgag-atctataaattgttt-cagGTAATTTCGGGCAAGTTATATGCTGGCCCTGAAGTAGATGTCTGGAGCTGTGGTGTGATACTCTACGCTCTTCTCTGTGGGACGCTTCCATTTGATGATG

upper sequence: GRMZM2G180704_T01 (Zea mays), 3'ss of exon 4
lower sequence: AT3G29160.2 (Arabidopsis thaliana), 3'ss of exon 4
gtaagctttctataataggtcaaagatataaagaggacccattagatcagtatggccgtatttcctacccctttgttggcaggcagtacagtatccttttattttctgcagGTGATATCTGGTAAACTATATGCTGGACCTGAAGTTGATGTGTGGAGCTGTGGGGTTATTCTTTATGCTCTTTTATGTGGTACTCTGCCATTTGATGACG
        | |||| |     |||| ||   |   |     ||  | |  | || |  | | || |  | |||         |  ||    | || |  |  ||  || |||| ||||| |||||| ||||||||||||||||||| ||||| ||||| || || |||||  | || ||||| ||||| |||||||| || |||||||| |
-------gtatatagtttagtaaagttactgaattg---tttttcacctatgtgactatgtctcgtttctctt-----atgagt-gtcttatctcttacttcttgttgtagGTTATATCAGGTAAATTATATGCTGGACCTGAAGTAGATGTATGGAGTTGCGGAGTTATATTGTACGCTCTATTATGCGGTACTCTTCCTTTTGATGATG

upper sequence: GRMZM2G180704_T01 (Zea mays), 3'ss of exon 4
lower sequence: Vv14s0108g01230.t01 (Vitis vinifera), 3'ss of exon 4
----------gtaagctttctataataggtcaaa----gatataaagaggacccattagat-cagtatggccgtatttcctacccctttgttggcaggcagtacagtatccttttattttc-----tgcagGTGATATCTGGTAAACTATATGCTGGACCTGAAGTTGATGTGTGGAGCTGTGGGGTTATTCTTTATGCTCTTTTATGTGGTACTCTGCCATTTGATGACG
             ||| || ||  ||| | |||      || |   |  ||   || || | || ||    |  || |   |      || | | |     ||  ||     ||  | | |     |  |||| |||||||| | | | || || |||||||| || ||||| |||||||| || |||||| | || |||||| | ||||||||||| ||||||||||| |
gtaaggagtttgcagcattataatataagacaattcctaatttttggttgagagatgagttacaatactttctaatatatgatgataatggttgaaatttctaaggttctaattagtgtcccattttatagGTTATATCTGGAAGATTGTACGCAGGACCTGAGGTGGATGTATGGAGCTGCGGTGTTATTTTGTACGCTCTTCTTTGTGGTACTCTTCCATTTGATGATG

upper sequence: GRMZM2G180704_T01 (Zea mays), 3'ss of exon 4
lower sequence: PP1S28_12V6.1 (Physcomitrella patens), 3'ss of exon 3
---------------------------------------------gtaagct--ttctataataggtcaaagatataaa-gaggacccattagatcagtatggccgtatttcctaccc--------ctttgttggcaggcagtacagtatccttttattttctgcagGTGATATCTGGTAAACTATATGCTGGACCTGAAGTTGATGTGTGGAGCTGTGGGGTTATTCTTTATGCTCTTTTATGTGGTACTCTGCCATTTGATGACG
                                             || |  |  || | | | | ||    | | |    |  |      |  | ||   ||   || ||   | |||           || | |  | | ||    |||  ||  |     ||||||| || || || ||  ||||||| || || || || ||||||||||||||||| |||||||| ||||||||||| |||||| || | || ||||| ||||
gttttgctctatgcctgattgccttgtttgacactgttttaattcgtcatgtgattgtgtcacatgtttctgttttctgtgttgggtgcctgaaccaagttgtaggttttctgtgcccggacacactcctgcttgttgactgt-tgatattgttgaac---atgcagGTCATTTCAGGGAAGTTATATGCCGGTCCCGAGGTGGATGTGTGGAGCTGTGGCGTTATTCTGTATGCTCTTTTGTGTGGTTCTTTACCCTTTGACGACG

upper sequence: GRMZM2G180704_T01 (Zea mays), 3'ss of exon 4
lower sequence: PP1S7_365V6.1 (Physcomitrella patens), 3'ss of exon 3
gtaagctttctataataggtcaaagatataaagaggacccattagatcagtatggccgtatttcctacccctttgttggcaggcagtacagtatccttttattttctgcagGTGATATCTGGTAAACTATATGCTGGACCTGAAGTTGATGTGTGGAGCTGTGGGGTTATTCTTTATGCTCTTTTATGTGGTACTCTGCCATTTGATGACG
     | || || ||    ||||||  |||      | |  || |  ||   | |  ||||||   |   |  | |||            |||| |||  |    |||||||| ||||| || || || ||||| || ||||| || || || ||||||||||| |||||||| |||||||| || |||||  |  |||| || || ||||
----acattgtacaaatcctcaaag-catatgctaaatct-tttgtgcatagttgtagtattt--aagttcagtcttgtatattgactttgtatgcttaaaa---ctgcagGTTATATCAGGGAAGCTCTATGCCGGTCCTGAGGTGGACGTCTGGAGCTGTGGCGTTATTCTGTATGCTCTCTTGTGTGGCTCGTTGCCCTTCGACGACG

upper sequence: GRMZM2G180704_T01 (Zea mays), 3'ss of exon 4
lower sequence: EFJ17922 (Selaginella moellendorffii), 3'ss of exon 3
gtaagctttctataataggtcaaagatataaagaggacccattagatcagtatggccgtatttcctacccctttgttggcaggcagtacagtatccttttattttctgcagGTGATATCTGGTAAACTATATGCTGGACCTGAAGTTGATGTGTGGAGCTGTGGGGTTATTCTTTATGCTCTTTTATGTGGTACTCTGCCATTTGATGACG
                                              |||||||  | | ||    |    | | |  |   | || |  |   |   ||| |      |||||||| || ||||| || ||||||||||| ||||| || || |||||||||||||| || || || || ||| | ||||| |  || || ||||| ||||
---------------------------------------------gtcagtatatcaggataagttttgtcatag--gctcgtcattctaagttgtctttctcaatcacagGTGATTTCCGGTAAGCTCTATGCTGGACCAGAAGTAGACGTATGGAGCTGTGGGGTGATACTATACGCACTTCTCTGTGGCAGCCTTCCCTTTGACGACG

upper sequence: GRMZM2G180704_T01 (Zea mays), 3'ss of exon 4
lower sequence: EFJ16445 (Selaginella moellendorffii), 3'ss of exon 3
gtaagctttctataataggtcaaagatataaagaggacccattagatcagtatggccgtatttcctacccctttgttggcagg-cagtacagtatccttttattttctgcagGTGATATCTGGTAAACTATATGCTGGACCTGAAGTTGATGTGTGGAGCTGTGGGGTTATTCTTTATGCTCTTTTATGTGGTACTCTGCCATTTGATGACG
                                              |||||||  | ||||           || | |||  | || |  |   |   ||| |      |||||||| || ||||| || ||||||||||| ||||| || || |||||||||||||| || || || || ||| | ||||| |  || || ||||| ||||
---------------------------------------------gtcagtatatcagtata---agttttgttataggctcgtcattctaagttgtctttctcaatcacagGTGATTTCCGGTAAGCTCTATGCTGGACCAGAAGTAGACGTATGGAGCTGTGGGGTGATACTATACGCACTTCTCTGTGGCAGCCTTCCCTTTGACGACG

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|71768950|gb|DR966887.1|DR966887
EST:     GTCATTTTCTGAAGACAAGTTGTGGTAGCCCAAATTATGCTGCTCCTGAG                         GTGATATCTGGTAAACTATATGCTGGACCTGAAGTTGATGTGTGGAGCTGT
genomic: GTCATTTTCTGAAGACAAGTTGTGGTAGCCCAAATTATGCTGCTCCTGAGgtaagctttc ... ttttctgcagGTGATATCTGGTAAACTATATGCTGGACCTGAAGTTGATGTGTGGAGCTGT
EST: gi|211439527|gb|FL064919.1|FL064919
EST:     TCATTTTCTGAAGACAAGTTGTGGTAGCCCAAATTATGCTGCTCCTGGAG                         -TGATATCTGGGTAA-CTATATGCTGGACCTGAAGTTGATGTGTGGAGCT
genomic: TCATTTTCTGAAGACAAGTTGTGGTAGCCCAAATTATGCTGCTCCTG-AGgtaagctttc ... ttttctgcagGTGATATCTGG-TAAACTATATGCTGGACCTGAAGTTGATGTGTGGAGCT
EST: gi|148969836|gb|EE020728.2|EE020728
EST:     GTCATTTTCTGAAGACAAGTTGTGGTAGCCCAAATTATGCTGCTCCTGAG                         GTGATATCTGGTAAACTATATGCTGGACCTGAAGTTGATGTGTGGAGCTGT
genomic: GTCATTTTCTGAAGACAAGTTGTGGTAGCCCAAATTATGCTGCTCCTGAGgtaagctttc ... ttttctgcagGTGATATCTGGTAAACTATATGCTGGACCTGAAGTTGATGTGTGGAGCTGT
EST: gi|149088708|gb|EE177828.2|EE177828
EST:     GTCATTTTCTGAAGACAAGTTGTGGTAGCCCAAATTATGCTGCTCCTGAG                         GTGATATCTGGTAAACTATATGCTGGACCTGAAGTTGATGTGTGGAGCTGT
genomic: GTCATTTTCTGAAGACAAGTTGTGGTAGCCCAAATTATGCTGCTCCTGAGgtaagctttc ... ttttctgcagGTGATATCTGGTAAACTATATGCTGGACCTGAAGTTGATGTGTGGAGCTGT
EST: gi|149088317|gb|EE177414.2|EE177414
EST:     GTCATTTTCTGAAGACAAGTTGTGGTAGCCCAAATTATGCTGCTCCTGAG                         GTGATATCTGGTAAACTATATGCTGGACCTGAAGTTGATGTGTGGAGCTGT
genomic: GTCATTTTCTGAAGACAAGTTGTGGTAGCCCAAATTATGCTGCTCCTGAGgtaagctttc ... ttttctgcagGTGATATCTGGTAAACTATATGCTGGACCTGAAGTTGATGTGTGGAGCTGT
EST: gi|211006231|gb|FL064937.1|FL064937
EST:     GTCATTTTCTGAAGACAAGTTGTGGTAGCCCAAAT-ATGCTGCTCCTGAG                         GTGATATCTGGTAAACTATATGCTGGACCTGAAAGT-GATGTGT
genomic: GTCATTTTCTGAAGACAAGTTGTGGTAGCCCAAATTATGCTGCTCCTGAGgtaagctttc ... ttttctgcagGTGATATCTGGTAAACTATATGCTGGACCTGAA-GTTGATGTGT
EST: gi|148974739|gb|EE025550.2|EE025550
EST:     GTCATTTTCTGAAGACAAGTTGTGGTAGCCCAAATTATGCTGCTCCTGAG                         GTGATATCTGGTAAACTATATGCTGGACCTGAAGTTGATGTGTGGAGCTGT
genomic: GTCATTTTCTGAAGACAAGTTGTGGTAGCCCAAATTATGCTGCTCCTGAGgtaagctttc ... ttttctgcagGTGATATCTGGTAAACTATATGCTGGACCTGAAGTTGATGTGTGGAGCTGT
EST: gi|211324790|gb|FL345978.1|FL345978
EST:     GTCATTTTCTGAAGACAAGTTGTGGTAGCCCAAATTATGCTGCTCCTGAG                         GTGATATCTGGTAAACTATATGCTGGACCTGAAGTTGATGTGTGGAGCTGT
genomic: GTCATTTTCTGAAGACAAGTTGTGGTAGCCCAAATTATGCTGCTCCTGAGgtaagctttc ... ttttctgcagGTGATATCTGGTAAACTATATGCTGGACCTGAAGTTGATGTGTGGAGCTGT

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: 47 (upstream exon), 48 (downstream exon)
Score: 321

ATGCAATGTTAAGATTGCAGATTTTGGCTTAAGTAATGTTATGCGGGATGGTCATTTTCTGAAGACAAGTTGTGGTAGCCCAAATTATGCTGCTCCTGAGgtaagctttc ... ttttctgcagGTGATATCTGGTAAACTATATGCTGGACCTGAAGTTGATGTGTGGAGCTGTGGGGTTATTCTTTATGCTCTTTTATGTGGTACTCTGCCATTTGATGACG


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 193

ATGCAATGTTAAGATTGCAGATTTTGGCTTAAGTAATGTTATGCGGGATGGTCATTTTCTGAAGACAAGTTGTGGTAGCCCAAATTATGCTGCTCCTGAGgtaagctttc ... ttttctgcagGTGATATCTGGTAAACTATATGCTGGACCTGAAGTTGATGTGTGGAGCTGTGGGGTTATTCTTTATGCTCTTTTATGTGGTACTCTGCCATTTGATGACG


Block sizes: 48 (upstream exon), 48 (downstream exon)
Score: 173

ATGCAATGTTAAGATTGCAGATTTTGGCTTAAGTAATGTTATGCGGGATGGTCATTTTCTGAAGACAAGTTGTGGTAGCCCAAATTATGCTGCTCCTGAGgtaagctttc ... ttttctgcagGTGATATCTGGTAAACTATATGCTGGACCTGAAGTTGATGTGTGGAGCTGTGGGGTTATTCTTTATGCTCTTTTATGTGGTACTCTGCCATTTGATGACG


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 429

ATGCAATGTTAAGATTGCAGATTTTGGCTTAAGTAATGTTATGCGGGATGGTCATTTTCTGAAGACAAGTTGTGGTAGCCCAAATTATGCTGCTCCTGAGgtaagctttc ... ttttctgcagGTGATATCTGGTAAACTATATGCTGGACCTGAAGTTGATGTGTGGAGCTGTGGGGTTATTCTTTATGCTCTTTTATGTGGTACTCTGCCATTTGATGACG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cgtatttcctacccctttgttggcaggcagtacagtatccttttattttctgcagGTGATATCTGGTAAACTATATGCTGGACCTGAAGTTGATGTGTGGAGCTGTGGGGTTATTCTTTATGCTCTTTTATGTGGTACTCTGCCATTTGATGACG
                                   tatccttttattttct  CT-rich tract
                                   tatccttttatttt  TA-rich tract