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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagcaagcatatcataaatgtcctcatgtgttttctttagcattgcatctggcattgtgttgtttatcgtgctgtgctacatttgcatgcgcataattatacatattagttagtgtgttgcatttgtttggttagaaattgacttaccctgatgcataacttacacagcttaactgtttcagATAATAAATGTGTATAATCAAGAATACGAGAGTGCAGCAGCATTTTGGCCAAGTGTTCATGGACGCATAATCACAGCGTTGATTGTATCACAGCTGCTTC

Basic information

species Zea mays
transcript GRMZM2G064189_T01
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G064189_T01 (Zea mays), 3'ss of exon 3
lower sequence: LOC_Os01g35050.4 (Oryza sativa), 3'ss of exon 10
gtaagcaagcatatcataaatgtcctcatgtgttttctttagcattgcatctggcattgtgttgtttatcgtgctgtgctacatttgcatgcgcataattatacatattagttagtgtgttgcatttgtttggttagaaattgacttaccctgatgcataacttacacagcttaactgtttcagATAATAAATGTGTATAATCAAGAATACGAGAGTGCAGCAGCATTTTGGCCAAGTGTTCATGGACGCATAATCACAGCGTTGATTGTATCACAGCTGCTTC
                                                                          ||||  ||| ||   |   |      ||| | |  ||| | |    | ||||    || |||   ||| |  |       | | ||||| |    | || | |||||||||||||||||||||| || |||||||| || |||||||||||||||||||||||||||||||||||||||||   ||| || || ||||||||||||||||
--------------------------------------------------------------------------tgtgtgacaatttagtcttcggtgcaataga-acaagtaatt---ctacattc---tgattatgtattaaaatgattgacttcctaactga---gggttcattgtttcagATAATAAATGTGTACAACCAAGAATATGAAAGTGCAGCAGCATTTTGGCCAAGTGTTCATGGACGCATAATTGTAGCATTAATCGTATCACAGCTGCTTC

upper sequence: GRMZM2G064189_T01 (Zea mays), 3'ss of exon 3
lower sequence: GLYMA17G01400.1 (Glycine max), 3'ss of exon 9
gtaagcaagcatatcataaatgtcctcatgtgttttctttagcattgcatctggcattgtgttgtttatcgtgctgtgctacatttgcatgcgcataattatacatattagttagtgtgttgcatttgtttggttagaaattgacttaccctgatgcataacttacaca-----gcttaactgtttcagATAATAAATGTGTATAATCAAGAATACGAGAGTGCAGCAGCATTTTGGCCAAGTGTTCATGGACGCATAATCACAGCGTTGATTGTATCACAGCTGCTTC
                                                                        |  || | |   |   |     ||| |||| ||| | |     ||  ||| |||  ||  ||     |||    |  ||  ||  |||| ||  | |      |||  |  || ||||| || ||||| ||||||||||| ||||||||||  |||||||| |||||   ||| |||   ||  | || |  ||  |||| || |||||| |  |||
------------------------------------------------------------------------gtagttccaagatgttagaattata-ttattcatgtcaaaggatg-attgtattatttgagtcccctatttttgttgccatatatataagttgaagacacctactttccaattgcagATTATCAATGTTTATAATCAAGAGTACGAGAGTGGTGCAGCATTCTGGCCTGATGTCCATTTTCGTGTCATTATTGCACTGATAGTGTCACAGATAGTTC

upper sequence: GRMZM2G064189_T01 (Zea mays), 3'ss of exon 3
lower sequence: GLYMA07G39320.1 (Glycine max), 3'ss of exon 10
gtaagcaagcatatcataaatgtcctcatgtgttttctttagcattgcatctggcattgtgttgtttatcgtgctgtgctacatttgcatgcgcataattatacatattagttagtgtg-ttgcatttgtttggttagaaattgacttaccctgatgcataacttacaca-----gcttaactgtttcagATAATAAATGTGTATAATCAAGAATACGAGAGTGCAGCAGCATTTTGGCCAAGTGTTCATGGACGCATAATCACAGCGTTGATTGTATCACAGCTGCTTC
                                                                        |  || | |   |   |     ||| |||||||  | |   ||| || ||| |||  ||  ||     |||    |  ||  ||  ||||  |  | |      |||  |  || ||||| || ||||| ||||||||||| ||||||||||  |||||||| |||||   ||| |||   ||  | || |  ||  |||| || |||||| |  |||
------------------------------------------------------------------------gtagttccaagatgttagaattata-ttatacacgtcaa--agtatgattgtattatttgagtcccctatttttgttgccatatatataaggtgaagacacctactttccaattgcagATTATCAATGTTTATAATCAAGAGTACGAGAGTGGTGCAGCATTCTGGCCTGATGTCCATTTTCGTGTCATTATTGCACTGATAGTGTCACAGATAGTTC

upper sequence: GRMZM2G064189_T01 (Zea mays), 3'ss of exon 3
lower sequence: AT4G22120.1 (Arabidopsis thaliana), 3'ss of exon 8
gtaagcaagcatatcataaatgtcctcatgtgttttctttagcattgcatctggcattgtgttgtttatcgtgctgtgctacatttgcatgcgcataattatacatattagttagtgtgttgcatttgtttggttagaaattgacttaccctgatgca-taacttacacag---cttaactgtttcagATAATAAATGTGTATAATCAAGAATACGAGAGTGCAGCAGCATTTTGGCCAAGTGTTCATGGACGCATAATCACAGCGTTGATTGTATCACAGCTGCTTC
                                                                                                              || ||| | ||    ||   |   |||      | ||    | | ||| |  |||| |||     ||   | | |||||| || || || || |||||||||||||||||||| ||||| |||||||||   |||||||||||  | ||  |||| ||| |  |||||||| ||||||
--------------------------------------------------------------------------------------------------------------gtaagtttcttcttctttccttaatagggtcgaatttgttttaaagcagtttcttaaacaaatttttgtttctgtcagATCATTAACGTATACAATCAAGAATACGAGAGTGCTGCAGCGTTTTGGCCAGACGTTCATGGACGAGTCATAGCAGCATTGGTAATATCACAGTTGCTTC

upper sequence: GRMZM2G064189_T01 (Zea mays), 3'ss of exon 3
lower sequence: AT4G04340.1 (Arabidopsis thaliana), 3'ss of exon 10
gtaagcaagcatatcataaatgtcctcatgtgttttctttagcattgcatctggcattgtgttgtttatcgtgctgtgctacatttgcatgcgcataattatacatattagttagtgtgttgcatttgtttggttagaaattgacttaccctgatgcataacttacacagcttaactgtttcagATAATAAATGTGTATAATCAAGAATACGAGAGTGCAGCAGCATTTTGGCCAAGTGTTCATGGACGCATAATCACAGCGTTGATTGTATCACAGCTGCTTC
                                                                                         |     || ||        |  | | | || || |  ||  | ||| ||   | ||||      |        |||      ||     | |||||| |||||||||||||||||||| || ||||| || || || ||||||||   ||||||||||||  | || || || |||||  |||| ||| ||||||
----------------------------------------------------------------------------------------gtaaatgtagtttctttctctcctaaatttgatgaaactggctagtttga---taacttg----aaccttctgtttatttgttttcttattctcagATCATAAATGTGTATAATCAAGAGTATGAGAGCGCTGCTGCGTTTTGGCCGGATGTTCATGGACGGGTTATAACGGCATTGATCATATCTCAGTTGCTTC

upper sequence: GRMZM2G064189_T01 (Zea mays), 3'ss of exon 3
lower sequence: AT3G21620.1 (Arabidopsis thaliana), 3'ss of exon 9
gtaagcaagcatatcataaatgtcctcatgtgttttctttagcattgcatctggcattgtgttgtttatcgtgctgtgctacatttgcatgcgcataattatacatattagttagtgtgttgcatttgtttggttagaaattgacttaccctgatgcataacttacacagct-taactgtttcagATAATAAATGTGTATAATCAAGAATACGAGAGTGCAGCAGCATTTTGGCCAAGTGTTCATGGACGCATAATCACAGCGTTGATTGTATCACAGCTGCTTC
                                                                                                  ||  | |    | | |  |  |  | | || ||  ||  | |||   |||     |||| |||   ||  || | |   |||| ||||| |||||||||||||| ||||| || |||||||| ||||| || ||||||  ||||||| ||||  || | |  ||  |||| ||||| ||||| ||| 
-------------------------------------------------------------------------------------------------gtttaaaacccaaatcacagaat--cctctgcttctttctatattctattat----atgcttaagaaactaagttctttttgttgcagATTATAAATGTGTATAACCAAGAGTATGAGAGTGCTGCAGCGTTCTGGCCAGATGTTCATAGACGTGTAGTGATTGCACTGATCGTATCTCAGCTTCTTT

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|78021094|gb|DV489481.1|DV489481
EST:     TGTATACCGCCACCAG                         ATAATAAATGTGTATAATCAAGAATACGAGAGTGCAGCAGCATTTTGGCCA
genomic: TGTATACCGCCACCAGgtaagcaagc ... actgtttcagATAATAAATGTGTATAATCAAGAATACGAGAGTGCAGCAGCATTTTGGCCA
EST: gi|5846752|gb|AI999835.1|AI999835
EST:     CTTTTGTATTGATATTCTTTGGGTTTGCGTACGTTGTATACCGCCACCAG                         ATAATAAATGTGTATAATCAAGAATACGAGAGTGCAGCAGCATTTTGGCCA
genomic: CTTTTGTATTGATATTCTTTGGGTTTGCGTACGTTGTATACCGCCACCAGgtaagcaagc ... actgtttcagATAATAAATGTGTATAATCAAGAATACGAGAGTGCAGCAGCATTTTGGCCA
EST: gi|5847484|gb|AW000563.1|AW000563
EST:     CTTTTGTATTGATATTCTTTGGGTTTGCGTACGTTGTATACCGCCACCAG                         ATAATAAATGTGTATAATCAAGAATACGAGAGTGCAGCAGCATTTTGGCCA
genomic: CTTTTGTATTGATATTCTTTGGGTTTGCGTACGTTGTATACCGCCACCAGgtaagcaagc ... actgtttcagATAATAAATGTGTATAATCAAGAATACGAGAGTGCAGCAGCATTTTGGCCA
EST: gi|40336310|gb|CK370380.1|CK370380
EST:     CTTTTGTATTGGTATTCTTTGGGTTTGCGTACGTTGTATACCGCCACCAG                         ATAATAAATGTGTATAATCAAGAATACGAGAGTGCAGCAGCATTTTGGCCA
genomic: CTTTTGTATTGATATTCTTTGGGTTTGCGTACGTTGTATACCGCCACCAGgtaagcaagc ... actgtttcagATAATAAATGTGTATAATCAAGAATACGAGAGTGCAGCAGCATTTTGGCCA
EST: gi|5055562|gb|AI734449.1|AI734449
EST:     CTTTGGGTTTGCGTACGTTGTATACCGCCACCAG                         ATAATAAATGTGTATAATCAAGAATACGAGAGTGCAGCAGCATTTTGGCCA
genomic: CTTTGGGTTTGCGTACGTTGTATACCGCCACCAGgtaagcaagc ... actgtttcagATAATAAATGTGTATAATCAAGAATACGAGAGTGCAGCAGCATTTTGGCCA
EST: gi|211159706|gb|FL164258.1|FL164258
EST:     CTTTTGTATTGATATTCTTTGGGTTTGCGTACGTTGTATACCGCCACCAG                         ATAATAAATGTGTATAATCAAGAATACGAGAGTGCAGCAGCATTTTGGCCA
genomic: CTTTTGTATTGATATTCTTTGGGTTTGCGTACGTTGTATACCGCCACCAGgtaagcaagc ... actgtttcagATAATAAATGTGTATAATCAAGAATACGAGAGTGCAGCAGCATTTTGGCCA
EST: gi|67022912|gb|CO451661.1|CO451661
EST:     CTTTTGTATTGATATTCTTTGGGGTTGCGTACGTTGTATACCGCCACCAG                         ATAATAAATGTGTATAATCAAGAATACGAGAGTGCAGCAGCATTTTGGCCA
genomic: CTTTTGTATTGATATTCTTTGGGTTTGCGTACGTTGTATACCGCCACCAGgtaagcaagc ... actgtttcagATAATAAATGTGTATAATCAAGAATACGAGAGTGCAGCAGCATTTTGGCCA
EST: gi|37392989|gb|CF633749.1|CF633749
EST:     CTTTTGTATTGGTATTCTTTGGGTTTGCGTACGTTGTATACCGCCACCAG                         ATAATAAATGTGTATAATCAAGAATACGAGAGTGCAGCAGCATTTTGGCCA
genomic: CTTTTGTATTGATATTCTTTGGGTTTGCGTACGTTGTATACCGCCACCAGgtaagcaagc ... actgtttcagATAATAAATGTGTATAATCAAGAATACGAGAGTGCAGCAGCATTTTGGCCA
EST: gi|74035115|gb|DT535605.1|DT535605
EST:     CTTTTGTATTGGTATTCTTTGGGTTTGCGTACGTTGTATACCGCCACCAG                         ATAATAAAGGTGTATAATCAAGAATACGAGAGTGCAGCAGCATTTTGGCCA
genomic: CTTTTGTATTGATATTCTTTGGGTTTGCGTACGTTGTATACCGCCACCAGgtaagcaagc ... actgtttcagATAATAAATGTGTATAATCAAGAATACGAGAGTGCAGCAGCATTTTGGCCA
EST: gi|211159704|gb|FL164256.1|FL164256
EST:     CTTTTGTATTGATATTCTTTGGGTTTGCGTACGTTGTATACCGCCACCAG                         ATAATAAATGTGTATAATCAAGAATACGAGAGTGCAGCAGCATTTTGGCCA
genomic: CTTTTGTATTGATATTCTTTGGGTTTGCGTACGTTGTATACCGCCACCAGgtaagcaagc ... actgtttcagATAATAAATGTGTATAATCAAGAATACGAGAGTGCAGCAGCATTTTGGCCA
EST: gi|60338400|gb|DN205373.1|DN205373
EST:     CTTTTGTATTGATATTCTTTGGGTTTGCGTACGTTGTATACCGCCACCAG                         ATAATAAATGTGTATAATCAAGAATACGAGAGTGCAGCAGCATTTTGGCCA
genomic: CTTTTGTATTGATATTCTTTGGGTTTGCGTACGTTGTATACCGCCACCAGgtaagcaagc ... actgtttcagATAATAAATGTGTATAATCAAGAATACGAGAGTGCAGCAGCATTTTGGCCA

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: 48 (upstream exon), 49 (downstream exon)
Score: 100

GTATTTCTTACTTGGTCTTGTCTATGCGGCAGTGACACCATTTTTGCTCCCTTTTGTATTGATATTCTTTGGGTTTGCGTACGTTGTATACCGCCACCAGgtaagcaagc ... actgtttcagATAATAAATGTGTATAATCAAGAATACGAGAGTGCAGCAGCATTTTGGCCAAGTGTTCATGGACGCATAATCACAGCGTTGATTGTATCACAGCTGCTTC


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 140

GTATTTCTTACTTGGTCTTGTCTATGCGGCAGTGACACCATTTTTGCTCCCTTTTGTATTGATATTCTTTGGGTTTGCGTACGTTGTATACCGCCACCAGgtaagcaagc ... actgtttcagATAATAAATGTGTATAATCAAGAATACGAGAGTGCAGCAGCATTTTGGCCAAGTGTTCATGGACGCATAATCACAGCGTTGATTGTATCACAGCTGCTTC


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 224

GTATTTCTTACTTGGTCTTGTCTATGCGGCAGTGACACCATTTTTGCTCCCTTTTGTATTGATATTCTTTGGGTTTGCGTACGTTGTATACCGCCACCAGgtaagcaagc ... actgtttcagATAATAAATGTGTATAATCAAGAATACGAGAGTGCAGCAGCATTTTGGCCAAGTGTTCATGGACGCATAATCACAGCGTTGATTGTATCACAGCTGCTTC


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 87

GTATTTCTTACTTGGTCTTGTCTATGCGGCAGTGACACCATTTTTGCTCCCTTTTGTATTGATATTCTTTGGGTTTGCGTACGTTGTATACCGCCACCAGgtaagcaagc ... actgtttcagATAATAAATGTGTATAATCAAGAATACGAGAGTGCAGCAGCATTTTGGCCAAGTGTTCATGGACGCATAATCACAGCGTTGATTGTATCACAGCTGCTTC




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttggttagaaattgacttaccctgatgcataacttacacagcttaactgtttcagATAATAAATGTGTATAATCAAGAATACGAGAGTGCAGCAGCATTTTGGCCAAGTGTTCATGGACGCATAATCACAGCGTTGATTGTATCACAGCTGCTTC
                                              ctgtttc  CT-rich tract
     tagaaatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaagcaagcatatcataaatgtcctcatgtgttttctttagcattgcatctggcattgtgttgtttatcgtgctgtgctacatttgcatgcgcataattatacatattagttagtgtgttgcatttgtttggttagaaattgacttaccctgatgcataacttacacagcttaactgtttcagATAATAAATGTGTATAATCAAGAATACGAGAGTGCAGCAGCATTTTGGCCAAGTGTTCATGGACGCATAATCACAGCGTTGATTGTATCACAGCTGCTTC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGCT