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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...cgtaggtcaagtttttttatacctgtattttttggcttatcatacagtctgctggttattctattcaggtttgctcaaagttgttttctctcgaatgcagGCTACGATTGGTATTGATTTCCTGTCAAAGACAATGTACCTTGAAGATAGAACTGTGAGACTCCAACTCTG

Basic information

species Zea mays
transcript GRMZM2G169694_T01
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G169694_T01 (Zea mays), 3'ss of exon 1
lower sequence: LOC_Os07g31370.1 (Oryza sativa), 3'ss of exon 1
-cgtaggtcaagtttttttatacctgtattttttggcttatcatacagtctgctggttattctattcaggtttgctca-aagttgttttctctcgaatgcagGCTACGATTGGTATTGATTTCCTGTCAAAGACAATGTACCTTGAAGATAGAACTGTGAGACTCCAACTCTG
 |   | |  ||||||   |||| | | ||     | ||    |  | |       ||||    |     | | ||||  | || || | | | |    |||||||| || |||||||| |||||||||||||||||||||||||||||||| ||||| ||||| ||||| ||
gcaatgtttcagtttta--atacttatcttaaaatgtttcagttttaatacttatcttatctggtcgttatgttctcatgatttattctattttgcgaacagGCTACAATCGGTATTGACTTCCTGTCAAAGACAATGTACCTTGAAGATAGGACTGTCAGACTGCAACTTTG

upper sequence: GRMZM2G169694_T01 (Zea mays), 3'ss of exon 1
lower sequence: GLYMA11G04330.1 (Glycine max), 3'ss of exon 1
-----cgtaggtcaagtttttttatacctgtattt-tttggctt-atcatacagtctgctggttattctattcaggtttgctcaaagttgttttctctcgaatgcagGCTACGATTGGTATTGATTTCCTGTCAAAGACAATGTACCTTGAAGATAGAACTGTGAGACTCCAACTCTG
       |   |   |  | | | ||  | ||||| ||| |||| ||  |||   |   |  || ||  ||||| |||      |  ||| ||| ||||  ||||||||||| |||||||||||||| || ||||| || ||||| || |||||| |||||||  |||| ||  | ||
gcttctttgactgtggcctgtgtgtatttttatttctttagcttcattttactagcacatttttgttgaattcaagtt-----gatattgatttttctc--atgcagGCTACAATTGGTATTGATTTTCTATCAAAAACTATGTATCTCGAAGATCGAACTGTTCGACTGCAGTTGTG

upper sequence: GRMZM2G169694_T01 (Zea mays), 3'ss of exon 1
lower sequence: GLYMA01G41090.1 (Glycine max), 3'ss of exon 1
--cgtaggtcaagtttttttatacctgtattttttggcttatcatacagtctgctggttattctattcaggtttgctcaaagttgttttc--tctcgaatgcagGCTACGATTGGTATTGATTTCCTGTCAAAGACAATGTACCTTGAAGATAGAACTGTGAGACTCCAACTCTG
   ||     |||  |  |    | || |  |||| |||    || || | ||    ||  |||   | |   | || ||| || || |   | |      ||||| |||||||||||||||||  | ||||| || ||||| ||||||||| |||||||  | || || ||   
gttgtcttataagcataat-gctcttggaaatttttgctccatatccattttgtcattttctcttgcctg---ttcttaaacttattattaatttttcgaacagGCCACGATTGGTATTGATTTTTTATCAAAAACTATGTATCTTGAAGATCGAACTGTTCGGCTGCAGCT---

upper sequence: GRMZM2G169694_T01 (Zea mays), 3'ss of exon 1
lower sequence: GLYMA01G41100.1 (Glycine max), 3'ss of exon 1
--cgtaggtcaagtttttttatacctgtatttt-ttggcttat-catacagtctgctggttattctattcaggtttgctcaaagttgttttctctcgaatgcagGCTACGATTGGTATTGATTTCCTGTCAAAGACAATGTACCTTGAAGATAGAACTGTGAGACTCCAACTCTG
    |   |   |  | | | ||  | |||||  || |||| | | |||   |   |  || ||  |||||  |    |   | || ||| |||    ||||||||||| |||||||||||||| || ||||| || ||||| ||||||||| |||||||  |||| ||  | ||
tctttgactgtggcctgtgtgtatttttatttccttagcttgttcttactaacatatatttgttgaattcaaatagattttgatttttttcctc----atgcagGCTACAATTGGTATTGATTTTCTATCAAAAACTATGTATCTTGAAGATCGAACTGTTCGACTGCAGTTGTG

upper sequence: GRMZM2G169694_T01 (Zea mays), 3'ss of exon 1
lower sequence: AT2G44610.1 (Arabidopsis thaliana), 3'ss of exon 1
cgtaggtcaagttttt--ttatacctgtatttt-ttggcttatcatacagtctgctggttattctattcaggtttgctcaaagttgttttctctcg-aatg--cagGCTACGATTGGTATTGATTTCCTGTCAAAGACAATGTACCTTGAAGATAGAACTGTGAGACTCCAACTCTG
      | ||| |  |  | |||  || |   |  | ||||||| | || | | | |  | ||||        |   |     || | || | ||  |||   ||||| || |||||||||||||| || |||||||||||||||||||||||| |||| || ||||| ||  | ||
-----tttaagctcctaataatatgtgaaccatgcttgcttatcgt-cattttacagaatgttcttccttttctaagtagtttttatgttgtttcataatcatcagGCCACAATTGGTATTGATTTTCTATCAAAGACAATGTACCTTGAAGATCGAACGGTCAGACTTCAGTTGTG

upper sequence: GRMZM2G169694_T01 (Zea mays), 3'ss of exon 1
lower sequence: Vv15s0021g00640.t01 (Vitis vinifera), 3'ss of exon 1
cgtaggtcaagtttttttatacctgtattttttggcttatcatacagtctgctggttattctattcaggtttgctcaaagttgttttctc--tcga-atgcagGCTACGATTGGTATTGATTTCCTGTCAAAGACAATGTACCTTGAAGATAGAACTGTGAGACTCCAACTCTG
|  |    | ||   | |||||   ||  || |   |   ||||  |  ||||  || || ||||    ||| |  ||  |||| || |   | || || |||||||| |||||||| ||||| || |||||||| ||||||||||||||| | || ||  |  | ||||||||
ctaaatataggtagctgtatacacctagcttattcttctccataagg--tgctt-ttgttttattttctttttcctaagcttgtgttattaattgacatccagGCTACTATTGGTATCGATTTTCTATCAAAGACGATGTACCTTGAAGATCGGACGGTCCGTTTGCAACTCTG

upper sequence: GRMZM2G169694_T01 (Zea mays), 3'ss of exon 1
lower sequence: Vv02s0012g00710.t01 (Vitis vinifera), 3'ss of exon 1
cgtaggtcaagtttttttatacctgtattttttggcttatcatacagtctgctggttattctattca--ggtttgctcaaagttgttttctctcgaatg--cagGCTACGATTGGTATTGATTTCCTGTCAAAGACAATGTACCTTGAAGATAGAACTGTGAGACTCCAACTCTG
  |    ||    ||   | |  | ||  || |||   |   ||   || | || ||| | | | |     ||  || | |  | || |       |||  |||||||| ||||||||||||||||| |||||||| ||||| ||||||||| |||| ||  | || ||  | ||
-ctccaccactccttacaaaatatttagcttctgg---aatttaagctcaggtgtttagtttgtgcgtcatttaacttataccttttcttgaatttatgatcagGCTACAATTGGTATTGATTTCCTATCAAAGACCATGTATCTTGAAGATCGAACCGTTCGTCTGCAGTTGTG

upper sequence: GRMZM2G169694_T01 (Zea mays), 3'ss of exon 1
lower sequence: EDP09951 (Chlamydomonas reinhardtii), 3'ss of exon 2
cgtaggtcaagtttttttatacctgtattttttggcttatcatacagtctgctggttattctattcaggtttgctcaaagttgttttctctcgaatgcagGCTACGATTGGTATTGATTTCCTGTCAAAGACAATGTACCTTGAAGATAGAACTGTGAGACTCCAACTCTG
                                  || ||   | | |  |     |||        | |  ||  ||   || |    ||||   ||||||| || || |||||||| |||||||||||||| ||||||||||| ||  | |||||| | || || |||||
--------------------------------gtgcgtactctgc-gcatttcctttacaacgacaacgcctga-catgcttttgcggtctccg-tgcagGCCACCATCGGTATTGACTTCCTGTCAAAGACCATGTACCTTGAGGACCGCACTGTGCGCCTGCAGCTCTG

upper sequence: GRMZM2G169694_T01 (Zea mays), 3'ss of exon 1
lower sequence: PP1S12_267V6.1 (Physcomitrella patens), 3'ss of exon 2
----cgtaggtcaagtttttttatacctg--tattttttggcttatcatacagtctgctggttattctattcaggtttgctcaaagttgttttctctcgaatgcagGCTACGATTGGTATTGATTTCCTGTCAAAGACAATGTACCTTGAAGATAGAACTGTGAGACTCCAACTCTG
    | |  |  ||  | |  |  ||     |||| ||    || |||   |  || |    | |||| |   | | || | | |      || | | |  ||||||| || ||||| |||||||| || ||||| |||||||||||||||||  | || ||| | || || || ||
tgttcatgtgcgaaaatctgatgcacgaaaatattgttcaatttttca---aaacttcgaagtgttctgt--ggttatggtgataaccaaattttat-gtttgcagGCGACTATTGGCATTGATTTTCTTTCAAAAACAATGTACCTTGAAGACCGCACCGTGCGGCTACAGCTTTG

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|211199864|gb|FK959366.1|FK959366
EST:     CGAGCATCATCACCCGCTTCATGTACGACAAGTTCGATAACACCTACCAG                         GCTACGATTGGTATTGATTTCCTGTCAAAGACAATGTACCTTGAAGATAGA
genomic: CGAGCATCATCACCCGCTTCATGTACGACAAGTTCGATAACACCTACCAGgtacgacggc ... tcgaatgcagGCTACGATTGGTATTGATTTCCTGTCAAAGACAATGTACCTTGAAGATAGA
EST: gi|32919616|gb|CF024428.1|CF024428
EST:     CGAGCATCATCACCCGCTTCATGTACGACAAGTTCGATAACACCTACCAG                         GCTACGATTGGTATTGATTTCCTGTCAAAGACAATGTACCTTGAAGATAGA
genomic: CGAGCATCATCACCCGCTTCATGTACGACAAGTTCGATAACACCTACCAGgtacgacggc ... tcgaatgcagGCTACGATTGGTATTGATTTCCTGTCAAAGACAATGTACCTTGAAGATAGA
EST: gi|148970042|gb|EE020962.2|EE020962
EST:     CGAGCATCATCACCCGCTTCATGTACGACAAGTTCGATAACACCTACCAG                         GCTACGATTGGTATTGATTTCCTGTCAAAGACAATGTACCTTGAAGATAGA
genomic: CGAGCATCATCACCCGCTTCATGTACGACAAGTTCGATAACACCTACCAGgtacgacggc ... tcgaatgcagGCTACGATTGGTATTGATTTCCTGTCAAAGACAATGTACCTTGAAGATAGA
EST: gi|149085277|gb|EE174782.2|EE174782
EST:     CGAGCATCATCACCCGCTTCATGTACGACAAGTTCGATAACACCTACCAG                         GCTACGATTGGTATTGATTTCCTGTCAAAGACAATGTACCTTGAAGATAGA
genomic: CGAGCATCATCACCCGCTTCATGTACGACAAGTTCGATAACACCTACCAGgtacgacggc ... tcgaatgcagGCTACGATTGGTATTGATTTCCTGTCAAAGACAATGTACCTTGAAGATAGA
EST: gi|89251359|gb|DY623145.1|DY623145
EST:     CGAGCATCATCACCCGCTTCATGTACGACAAGTTCGATAACACCTACCAG                         GCTACGATTGGTATTGATTTCCTGTCAAAGACAATGTACCTTGAAGATAGA
genomic: CGAGCATCATCACCCGCTTCATGTACGACAAGTTCGATAACACCTACCAGgtacgacggc ... tcgaatgcagGCTACGATTGGTATTGATTTCCTGTCAAAGACAATGTACCTTGAAGATAGA
EST: gi|71333158|gb|DR803614.1|DR803614
EST:     CGAGCATCATCACCCGCTTCATGTACGACAAGTTCGATAACACCTACCAG                         GCTACGATTGGTATTGATTTCCTGTCAAAGACAATGTACCTTGAAGATAGA
genomic: CGAGCATCATCACCCGCTTCATGTACGACAAGTTCGATAACACCTACCAGgtacgacggc ... tcgaatgcagGCTACGATTGGTATTGATTTCCTGTCAAAGACAATGTACCTTGAAGATAGA
EST: gi|148960910|gb|EE011595.2|EE011595
EST:     CGAGCATCATCACCCGCTTCATGTACGACAAGTTCGATAACACCTACCAG                         GCTACGATTGGTATTGATTTCCTGTCAAAGACAATGTACCTTGAAGATAGA
genomic: CGAGCATCATCACCCGCTTCATGTACGACAAGTTCGATAACACCTACCAGgtacgacggc ... tcgaatgcagGCTACGATTGGTATTGATTTCCTGTCAAAGACAATGTACCTTGAAGATAGA
EST: gi|211199857|gb|FK959359.1|FK959359
EST:     CGAGCATCATCACCCTCTTCATGTACGACAAGTTCGATAACACCTACCAG                         GCTACGATTGGTATTGATTTCCTGTCAAAGACAATGTACCTTGAAGATAGA
genomic: CGAGCATCATCACCCGCTTCATGTACGACAAGTTCGATAACACCTACCAGgtacgacggc ... tcgaatgcagGCTACGATTGGTATTGATTTCCTGTCAAAGACAATGTACCTTGAAGATAGA
EST: gi|87152147|gb|DY396936.1|DY396936
EST:     CGAGCATCATCACCCGCTTCATGTACGACAAGTTCGATAACACCTACCAG                         GCTACGATTGGTATTGATTTCCTGTCAAAGACAATGTACCTTGAAGATAGA
genomic: CGAGCATCATCACCCGCTTCATGTACGACAAGTTCGATAACACCTACCAGgtacgacggc ... tcgaatgcagGCTACGATTGGTATTGATTTCCTGTCAAAGACAATGTACCTTGAAGATAGA
EST: gi|32870836|gb|CF010518.1|CF010518
EST:     GAGCATCATCACCCGCTTCATGTACGACAAGTGTCGATAACACCTACCAG                         GCTACGATTGGTATTGATTTCCTGTCAAAGACAATGTACCTTGAAGATAGA
genomic: GAGCATCATCACCCGCTTCATGTACGACAAGT-TCGATAACACCTACCAGgtacgacggc ... tcgaatgcagGCTACGATTGGTATTGATTTCCTGTCAAAGACAATGTACCTTGAAGATAGA

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), 47 (downstream exon)
Score: 196

GCTCGCCAAGTACAAGCTCGTCTTCCTGGGGGACCAGTCCGTCGGCAAGACGAGCATCATCACCCGCTTCATGTACGACAAGTTCGATAACACCTACCAGgtacgacggc ... tcgaatgcagGCTACGATTGGTATTGATTTCCTGTCAAAGACAATGTACCTTGAAGATAGAACTGTGAGACTCCAACTCTG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 173

GCTCGCCAAGTACAAGCTCGTCTTCCTGGGGGACCAGTCCGTCGGCAAGACGAGCATCATCACCCGCTTCATGTACGACAAGTTCGATAACACCTACCAGgtacgacggc ... tcgaatgcagGCTACGATTGGTATTGATTTCCTGTCAAAGACAATGTACCTTGAAGATAGAACTGTGAGACTCCAACTCTG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 191

GCTCGCCAAGTACAAGCTCGTCTTCCTGGGGGACCAGTCCGTCGGCAAGACGAGCATCATCACCCGCTTCATGTACGACAAGTTCGATAACACCTACCAGgtacgacggc ... tcgaatgcagGCTACGATTGGTATTGATTTCCTGTCAAAGACAATGTACCTTGAAGATAGAACTGTGAGACTCCAACTCTG


Block sizes: 49 (upstream exon), 47 (downstream exon)
Score: 225

GCTCGCCAAGTACAAGCTCGTCTTCCTGGGGGACCAGTCCGTCGGCAAGACGAGCATCATCACCCGCTTCATGTACGACAAGTTCGATAACACCTACCAGgtacgacggc ... tcgaatgcagGCTACGATTGGTATTGATTTCCTGTCAAAGACAATGTACCTTGAAGATAGAACTGTGAGACTCCAACTCTG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

agtctgctggttattctattcaggtttgctcaaagttgttttctctcgaatgcagGCTACGATTGGTATTGATTTCCTGTCAAAGACAATGTACCTTGAAGATAGAACTGTGAGACTCCAACTCTG
                                   ttgttttctctc  CT-rich tract
          ttattctatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
cgtaggtcaagtttttttatacctgtattttttggcttatcatacagtctgctggttattctattcaggtttgctcaaagttgttttctctcgaatgcagGCTACGATTGGTATTGATTTCCTGTCAAAGACAATGTACCTTGAAGATAGAACTGTGAGACTCCAACTCTG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGAAGA
- - - - - - - - - - acctgta
- - - - - - - - - - - - - - - - - - - - catacag
- - - - - - - - - - - - - - - - - - - - - - - -tctgctg