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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...atcgtagtagttatgatccaactatttactatcctacacttggagttctgacctgattcaggatcacgatctttaacaatcatgtgtggttaatttgcagGACCGTGATAGCTACTGGAAGATGATGCACAAATACATAGGATCAGATGTTACATCACTTGTGACACTTCCAGTCATAATTTTTGAGCCAATGACAATGC

Basic information

species Zea mays
transcript GRMZM2G174644_T02
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G174644_T01 (Zea mays), 3'ss of exon 2
lower sequence: LOC_Os03g16690.1 (Oryza sativa), 3'ss of exon 2
-atcgtagtagtt-atgatcc-aactatttactatccta--cacttggagttctgacctg-attcaggatcacgatctttaacaatcatgtgtggttaatttgcagGACCGTGATAGCTACTGGAAGATGATGCACAAATACATAGGATCAGATGTTACATCACTTGTGACACTTCCAGTCATAATTTTTGAGCCAATGACAATGC
 ||| |  |||   |||||   |||   ||  |||   |    |   | |||||    |  || |      | | ||||  ||| ||        ||||| ||||||| |||||||| || ||||||||||||||||| ||||||||  |||||||||||||||||||||||||||| ||||| ||||||||||||||||||||||
gatctttctagaggatgattggaacacctttgtatttcagctgcacagtgttctcgtgtatatcccttcatatgctctt-gacattc-----caattaatctgcagGATCGTGATAGTTATTGGAAGATGATGCACAAGTACATAGGGGCAGATGTTACATCACTTGTGACACTTCCGGTCATCATTTTTGAGCCAATGACAATGC

upper sequence: GRMZM2G174644_T01 (Zea mays), 3'ss of exon 2
lower sequence: GLYMA11G14770.1 (Glycine max), 3'ss of exon 2
-atcgtagtagttatgatccaactatttactatcctacacttggagttctgacctgattcaggatcacgatctttaacaatcatgtgtggtta-atttgcagGACCGTGATAGCTACTGGAAGATGATGCACAAATACATAGGATCAGATGTTACATCACTTGTGACACTTCCAGTCATAATTTTTGAGCCAATGACAATGC
 ||     |  |      |     || | |  || | ||   |   |  |   ||||  ||  || |     |||  |   | |  |   ||  || |  ||||  | ||| | ||||||||||||||||| || || || || || ||||| |||||| | |||||||| ||||| || || ||||| |||||||| ||| 
gatttcccttttctcttccttggcatatgcc-tcattcatacgtgctcatattctgaa-cattattatctcttttttctccctttggctcttgtatataaagGAAAGAGATGGTTACTGGAAGATGATGCAGAAGTATATTGGCTCGGATGTAACATCAATGGTGACACTACCAGTTATTATATTTGAACCAATGACTATGA

upper sequence: GRMZM2G174644_T01 (Zea mays), 3'ss of exon 2
lower sequence: GLYMA07G15930.3 (Glycine max), 3'ss of exon 2
-----atcgtagtagttatgatccaactatttactatcctacacttggagttctgacctgattcaggatcacgatctttaacaatcatgtgtggttaatttgcagGACCGTGATAGCTACTGGAAGATGATGCACAAATACATAGGATCAGATGTTACATCACTTGTGACACTTCCAGTCATAATTTTTGAGCCAATGACAATGC
     ||  ||    | ||| |  |  |    |  ||  |   | |  |  | |    ||  |||      | || ||||    || | |      | ||| ||||| || ||||| |||||||| |||||||| || ||  | || || ||| | |||||| | |||||||||||||| || |||||||| |||||||||||||
tttctattttatc--tcatggtggactttggaaaaattattttcctctatatttataatgtatcatttctgc-atgtttatt--tcctttacttacactttacagGAGCGAGATAGTTACTGGAAAATGATGCAAAAGTATGTTGGCTCTGATATCACATCAATGGTGACACTTCCAGTTATCATTTTTGAACCAATGACAATGC

upper sequence: GRMZM2G174644_T01 (Zea mays), 3'ss of exon 2
lower sequence: GLYMA18G39880.1 (Glycine max), 3'ss of exon 2
-----------atcgtagtagttatgatccaactatttactatcctacacttggagttctgacctgattcaggatcacgatctttaacaatcatgtgtggttaatttgcagGACCGTGATAGCTACTGGAAGATGATGCACAAATACATAGGATCAGATGTTACATCACTTGTGACACTTCCAGTCATAATTTTTGAGCCAATGACAATGC
           |||  | | || |   |   |  ||||  | |||| ||  |  | |  ||     |||| | ||    || |       | |  |    |||||    |||| || ||| | |||||||| |||||||| || ||  | || || ||| | |||||| | ||||||||||| || || ||||||||||||||||||||  
atttttattttatctca-tggtgaactttggagaatttcttttcctccatattta-taatgtatcaattctgcatgtttatttcct----ttacttacacttaat----aGGAGCGAGATGGTTACTGGAAAATGATGCAAAAGTATGTTGGCTCTGATATCACATCAATGGTGACACTTCCGGTTATCATTTTTGAGCCAATGACAATA-

upper sequence: GRMZM2G174644_T01 (Zea mays), 3'ss of exon 2
lower sequence: GLYMA15G04210.1 (Glycine max), 3'ss of exon 2
--atcgtagtagtt-atgatccaactatttactatcctacacttggagttctgacctgattcaggatcacgatctttaacaatcatgtgtggttaatttgcagGACCGTGATAGCTACTGGAAGATGATGCACAAATACATAGGATCAGATGTTACATCACTTGTGACACTTCCAGTCATAATTTTTGAGCCAATGACAATGC
   | ||  || || ||  || |  | | | ||     |||       | |  || | |||  |    |  || |||  | ||| | ||   ||  | | |||||  | ||| | ||||||||||||||||||||||| || || |||||||| |||||| | || ||||| ||||| || |||||||| |||||||| ||||
ttttggttttactttattttctatttttcttcttcagcacatacctgatgcatactttattgtga--tattattttttcctatc-tttgacttttgtatacagGAAAGAGATGGTTACTGGAAGATGATGCACAAATATATTGGCTCAGATGTAACATCAATGGTAACACTACCAGTTATTATTTTTGAACCAATGACTATGC

upper sequence: GRMZM2G174644_T01 (Zea mays), 3'ss of exon 2
lower sequence: AT5G59420.1 (Arabidopsis thaliana), 3'ss of exon 2
atcgtagtagttatgatccaac--tatttactatcctacacttggagttctgacctgattcaggatcacgatctttaacaatcatgtgtggttaatttgcagGACCGTGATAGCTACTGGAAGATGATGCACAAATACATAGGATCAGATGTTACATCACTTGTGACACTTCCAGTCATAATTTTTGAGCCAATGACAATGC
      |||  ||     | |   | | |   || || |   |  | |||     || |||   |       |    | | | |||| |   || ||   |||| || ||||| ||||||||||||||||| ||||| ||||| || ||| |||| ||| | ||||| ||||| ||  | || |||||||| ||||| ||||
------gtaactaatcgtcgatggtgtctttgatacttcttcttaaattcctctatgtttctctact-tacccgaagaaacttatgtttttgtatttaatagGAACGAGATAGTTACTGGAAGATGATGCAGAAATATATAGGTTCGGATATTACGTCAATGGTGACTCTTCCTGTTGTTATATTTGAGCCTATGACTATGC

upper sequence: GRMZM2G174644_T01 (Zea mays), 3'ss of exon 2
lower sequence: AT3G09300.1 (Arabidopsis thaliana), 3'ss of exon 2
atcgtagtagttatgatccaactatttactatcctacacttggagtt-ctgacctgattcaggatcacgatctttaacaatcatgtgtggttaatttgcagGACCGTGATAGCTACTGGAAGATGATGCACAAATACATAGGATCAGATGTTACATCACTTGTGACACTTCCAGTCATAATTTTTGAGCCAATGACAATGC
                |  |  || ||  |    |||  |||  |||  |||| | | |   ||||      | | | ||  ||        ||||   |||| || ||| |||| |||||||||||||| || ||||||||||| |||||||||||| | ||||| ||||| || || |||||||| |||||||||||||
---------------gtatatatacttcttcctttactattgttgttgttgacataactgttgatctaatcatctgagaaatatacac----aattcttagGATCGAGATGGCTATTGGAAGATGATGCAGAAGTACATAGGATCTGATGTTACATCAATGGTGACCCTTCCTGTGATTATTTTTGAACCAATGACAATGC

upper sequence: GRMZM2G174644_T01 (Zea mays), 3'ss of exon 2
lower sequence: AT5G02100.1 (Arabidopsis thaliana), 3'ss of exon 2
atcgtagtagttatgatccaactatttactatcctacacttggagttctgacctgattcaggatca----cgatctttaacaatcatgtgtgg--ttaatttg-cagGACCGTGATAGCTACTGGAAGATGATGCACAAATACATAGGATCAGATGTTACATCACTTGTGACACTTCCAGTCATAATTTTTGAGCCAATGACAATGC
    ||||  | ||   | ||  ||||       |   ||||  ||| | ||  || |  | |  |    |  |  |    | | || ||| |  || ||||  ||||| |||||| |||| |||||||||||||| || || ||||| || |||||||||||  | || || ||||| || || |||||||| || ||||||||| 
-gtatagtgctgatttactaaagatttctctctttgttcttgttgttgttacaagaattggaagaaaaaacagtactctggatttatatgttggcttgatttctcagGAACGTGATGGCTATTGGAAGATGATGCAGAAGTATATAGGGTCTGATGTTACATCTATGGTTACTCTTCCTGTGATCATTTTTGAACCCATGACAATGT

upper sequence: GRMZM2G174644_T01 (Zea mays), 3'ss of exon 2
lower sequence: Vv08s0007g00480.t01 (Vitis vinifera), 3'ss of exon 2
--atcgtagtagttatgatccaactatttactatcctacacttggagttctgacct--gattcaggatcacgatctttaacaatcatgtgtggttaatttgcagGACCGTGATAGCTACTGGAAGATGATGCACAAATACATAGGATCAGATGTTACATCACTTGTGACACTTCCAGTCATAATTTTTGAGCCAATGACAATGC
     ||  ||  |  |    ||      |  |  || | ||     || | || |  | ||   |||    || |||     | || |    ||  ||| |||||||| || || |||||||||||||||||||| || ||||| || ||||| |||||| | ||||||||||| || || |||||||||||  |||| || |
atggagtgataaattgggggaaaaagaaaagaaggcttctctgtatatttttacatatggttattgatgctcattttttgggttaattt----tttttttccagGACCGGGACAGTTACTGGAAGATGATGCACAAGTATATAGGCTCTGATGTCACATCAATGGTGACACTTCCTGTTATGATTTTTGAGCCGTTGACTATAC

upper sequence: GRMZM2G174644_T01 (Zea mays), 3'ss of exon 2
lower sequence: Vv06s0004g04930.t01 (Vitis vinifera), 3'ss of exon 2
atcgtagtagttatgatccaact-atttactatcctacacttggagttctgacctgattcaggatca----cgatctttaacaatcatgtgtggttaatttgcagGACCGTGATAGCTACTGGAAGATGATGCACAAATACATAGGATCAGATGTTACATCACTTGTGACACTTCCAGTCATAATTTTTGAGCCAATGACAATGC
       | ||  |||   | |  || |   ||| ||   | | | ||    |   |||    ||       ||| |||    | | |||   |||   ||| ||||  | || || ||||||||||||||||| || || ||||| |||||||| || ||| | ||||||||||||||  | ||||||||||||||||||||||
---aatcttgtcttgaattacccgatatgaaatcatattttagcaatttatcctgtattttttatttgtgctgatattt--tgagcttgttctgttttcttgtagGAAAGGGACAGTTACTGGAAGATGATGCAAAAGTATATAGGTTCAGATGTCACCTCAATGGTGACACTTCCAGTTCTGATTTTTGAGCCAATGACAATGC

upper sequence: GRMZM2G174644_T01 (Zea mays), 3'ss of exon 2
lower sequence: PP1S148_87V6.1 (Physcomitrella patens), 3'ss of exon 2
----------------------------------------------------------------------------------------atcgtagtagttatgatccaactatttactatcctacacttggagttctgacctgattcaggatcacgatctttaacaatcat-gtgtggttaatttgcagGACCGTGATAGCTACTGGAAGATGATGCACAAATACATAGGATCAGATGTTACATCACTTGTGACACTTCCAGTCATAATTTTTGAGCCAATGACAATGC
                                                                                        |  | | | |   | ||  ||||  |    |   |  |  || |    | |    ||       |      ||      |  |  |||||  | |  ||||||  | || || || ||||| ||||||||||| |||||||| || ||  |||| ||| | ||||||||||||||||| || |||||||| ||||| | ||
gtgaccttcatcttcatgccttaagcatcgagatcagtaatcatttttaatgtatgttgtggtgtggcattagtgccaatttcggcgaactggattggaattaatttaactcctcttgaattttaatgtgaaagaatcagtacatcggctgccttaccgttgggtttttgttatgtggcaagt--gcagGATAGAGAAAGTTATTGGAAAATGATGCACAAGTACATAGGTTCTGACATTACTTCAATGGTGACACTTCCAGTCATCATATTTGAGCCCATGACTACGC

upper sequence: GRMZM2G174644_T01 (Zea mays), 3'ss of exon 2
lower sequence: EFJ08612 (Selaginella moellendorffii), 3'ss of exon 2
atcgtagtagttatgatccaactatttactatcctacacttggagttct-gacctgattcaggatcacgatctttaacaatcatgtgtggttaatttgcagGACCGTGATAGCTACTGGAAGATGATGCACAAATACATAGGATCAGATGTTACATCACTTGTGACACTTCCAGTCATAATTTTTGAGCCAATGACAATGC
         || |   | |   | ||   | || |   |||  | | || |   |  ||      | |  |||||     | | |        ||    |||| ||||| ||||||||||| ||||||||||| || || ||||| || || || ||  | |||||||| |||||  | ||||||||||| ||||| ||||
---------gtaagtcttcccttgttctttttcttgttctttcaatacttgtttttgtttgtttcctcactctttggtctttacg--------atcgatagGATCGTGAGAGCTACTGGAAAATGATGCACAAGTATATTGGATCGGACGTCACTTCCATGGTGACACTGCCAGTTTTGATTTTTGAGCCCATGACGATGC

upper sequence: GRMZM2G174644_T01 (Zea mays), 3'ss of exon 2
lower sequence: EFJ19778 (Selaginella moellendorffii), 3'ss of exon 2
atcgtagtagttatgatccaactatttactatcctacacttggagttct-gacctgattcaggatcacgatctttaacaatcatgtgtggttaatttgcagGACCGTGATAGCTACTGGAAGATGATGCACAAATACATAGGATCAGATGTTACATCACTTGTGACACTTCCAGTCATAATTTTTGAGCCAATGACAATGC
         || |   | |   | ||   | || |   |||  | | || |   |  ||      | |  |||||     | | |        ||    |||| ||||| ||||||||||| ||||||||||| || || ||||| || || || ||  | |||||||| |||||  | ||||||||||| ||||| ||||
---------gtaagtcttcccttgttctttttcttgttcttttaatacttgtttttgtttgtttcctcactctttggtctttacg--------atcgatagGATCGTGAGAGCTACTGGAAAATGATGCACAAGTATATTGGATCGGACGTCACTTCCATGGTGACACTGCCAGTTTTGATTTTTGAGCCCATGACGATGC

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|13150716|gb|BG321038.1|BG321038
EST:     GCACAGATGATGCTGAAGAAGAAGCTTTGAAGGGGAGATGGAAGCAGGAG                         GACCGTGATAGCTACTGGAAGATGATGCACAAATACATAGGATCAGATGTT
genomic: GCACAGATGATGCTGAAGAAGAAGCTTTGAAGGGGAGATGGAAGCAGGAGgtaaggagat ... taatttgcagGACCGTGATAGCTACTGGAAGATGATGCACAAATACATAGGATCAGATGTT
EST: gi|211272002|gb|FK970185.1|FK970185
EST:     GCACAGATGATGCTGAAGAAGAAGCTTTGAAGGGGAGATGGAAGCAGGAG                         GACCGTGATAGCTACTGGAAGATGATGCACAAAT
genomic: GCACAGATGATGCTGAAGAAGAAGCTTTGAAGGGGAGATGGAAGCAGGAGgtaaggagat ... taatttgcagGACCGTGATAGCTACTGGAAGATGATGCACAAAT
EST: gi|211271996|gb|FK970179.1|FK970179
EST:     GCACAGATGATGCTGAAGAAGAAGCTTTGAAGGGGAGATGGAAGCAGGAG                         GAC-GTGATAGCTACTGGAAGATGATGCACAAATACATAG
genomic: GCACAGATGATGCTGAAGAAGAAGCTTTGAAGGGGAGATGGAAGCAGGAGgtaaggagat ... taatttgcagGACCGTGATAGCTACTGGAAGATGATGCACAAATACATAG
EST: gi|211271999|gb|FK970182.1|FK970182
EST:     GCACAGATGATGCTGAAGAAGAAGCTTTGAAGGGGAGATGGAAGCAGGAG                         GACCGTGATAGCTACTGGAAGATGATGCACAAATACATAGGATCAGATGTT
genomic: GCACAGATGATGCTGAAGAAGAAGCTTTGAAGGGGAGATGGAAGCAGGAGgtaaggagat ... taatttgcagGACCGTGATAGCTACTGGAAGATGATGCACAAATACATAGGATCAGATGTT
EST: gi|211271998|gb|FK970181.1|FK970181
EST:     GCACAGATGATGCTGAAGAAGAAGCTTTGAAGGGGAGATGGAAGCAGGAG                         GACCGTGATAGCTACTGGAAGATGATGCACAAATACATAGGATCAGATGTT
genomic: GCACAGATGATGCTGAAGAAGAAGCTTTGAAGGGGAGATGGAAGCAGGAGgtaaggagat ... taatttgcagGACCGTGATAGCTACTGGAAGATGATGCACAAATACATAGGATCAGATGTT
EST: gi|211272003|gb|FK970186.1|FK970186
EST:     GCACAGATGATGCTGAAGAAGAAGCTTTGAAGGGGAGATGGAAGCAGGAG                         GACCGTGATAGCTACTGGAAGATGATTGCACAAATACATAGGATCAGATGT
genomic: GCACAGATGATGCTGAAGAAGAAGCTTTGAAGGGGAGATGGAAGCAGGAGgtaaggagat ... taatttgcagGACCGTGATAGCTACTGGAAGATGAT-GCACAAATACATAGGATCAGATGT
EST: gi|149009147|gb|EE041283.2|EE041283
EST:     GCACAGATGATGCTGAAGAAGAAGCTTTGAAGGGGAGATGGAAGCAGGAG                         GACCGTGATAGCTACTGGAAGATGATGCACAAATACATAGGATCAGATGTT
genomic: GCACAGATGATGCTGAAGAAGAAGCTTTGAAGGGGAGATGGAAGCAGGAGgtaaggagat ... taatttgcagGACCGTGATAGCTACTGGAAGATGATGCACAAATACATAGGATCAGATGTT
EST: gi|18659308|gb|BM500269.1|BM500269
EST:     GCACAGATGATGCTGAAGAAGAAGCTTTGAAGGGGAGATGGAAGCAGGAG                         GACCGTGATAACTACTGGAAGATGATGCACAAATACATANGATCAGATGTT
genomic: GCACAGATGATGCTGAAGAAGAAGCTTTGAAGGGGAGATGGAAGCAGGAGgtaaggagat ... taatttgcagGACCGTGATAGCTACTGGAAGATGATGCACAAATACATAGGATCAGATGTT

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: 284

GCTGCTTGGTTATGAAGGCCTTGAAGTTATTAACCCCGATGGAGGCACAGATGATGCTGAAGAAGAAGCTTTGAAGGGGAGATGGAAGCAGGAGgtaaggagat ... taatttgcagGACCGTGATAGCTACTGGAAGATGATGCACAAATACATAGGATCAGATGTTACATCACTTGTGACACTTCCAGTCATAATTTTTGAGCCAATGACAATGC


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 966

GCTGCTTGGTTATGAAGGCCTTGAAGTTATTAACCCCGATGGAGGCACAGATGATGCTGAAGAAGAAGCTTTGAAGGGGAGATGGAAGCAGGAGgtaaggagat ... taatttgcagGACCGTGATAGCTACTGGAAGATGATGCACAAATACATAGGATCAGATGTTACATCACTTGTGACACTTCCAGTCATAATTTTTGAGCCAATGACAATGC


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 949

GCTGCTTGGTTATGAAGGCCTTGAAGTTATTAACCCCGATGGAGGCACAGATGATGCTGAAGAAGAAGCTTTGAAGGGGAGATGGAAGCAGGAGgtaaggagat ... taatttgcagGACCGTGATAGCTACTGGAAGATGATGCACAAATACATAGGATCAGATGTTACATCACTTGTGACACTTCCAGTCATAATTTTTGAGCCAATGACAATGC


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 502

GCTGCTTGGTTATGAAGGCCTTGAAGTTATTAACCCCGATGGAGGCACAGATGATGCTGAAGAAGAAGCTTTGAAGGGGAGATGGAAGCAGGAGgtaaggagat ... taatttgcagGACCGTGATAGCTACTGGAAGATGATGCACAAATACATAGGATCAGATGTTACATCACTTGTGACACTTCCAGTCATAATTTTTGAGCCAATGACAATGC




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttctgacctgattcaggatcacgatctttaacaatcatgtgtggttaatttgcagGACCGTGATAGCTACTGGAAGATGATGCACAAATACATAGGATCAGATGTTACATCACTTGTGACACTTCCAGTCATAATTTTTGAGCCAATGACAATGC
                          tttaacaat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
atcgtagtagttatgatccaactatttactatcctacacttggagttctgacctgattcaggatcacgatctttaacaatcatgtgtggttaatttgcagGACCGTGATAGCTACTGGAAGATGATGCACAAATACATAGGATCAGATGTTACATCACTTGTGACACTTCCAGTCATAATTTTTGAGCCAATGACAATGC

- - - - - - - - -ccaacta
- - - - - - - - - - - - - - - - cctacac
- - - - - - - - - - - - - - - - - - - - - - -ttctgac
- - - - - - - - - - - - - - - - - - - - - - - - - - -tgattca
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - catgtgt