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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tgtgaaactattgcatcctaaacagtccttgggcttttgtagagtttgtttcacattacacttacggggaagaattgacagtgttcctctgtttgaacagCTAAGTTTTGTGGACCTTGCTGGTTCTGAGAGGGTGAAAAAATCTGGTTCCGCAGGAAAGCAACTGAAAGAAGCACAAAGTATAAACAAATCTCTTTCTG

Basic information

species Zea mays
transcript GRMZM2G423861_T01
intron # 21
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G423861_T02 (Zea mays), 3'ss of exon 20
lower sequence: LOC_Os04g57140.2 (Oryza sativa), 3'ss of exon 21
tgtgaaactattgcatcctaaacagtccttgggcttttgtagagtttgtttcacattacacttacggggaagaattgacagtgt-----tcctctgtttgaacagCTAAGTTTTGTGGACCTTGCTGGTTCTGAGAGGGTGAAAAAATCTGGTTCCGCAGGAAAGCAACTGAAAGAAGCACAAAGTATAAACAAATCTCTTTCTG
     || || |  |   |||| |  |  ||  |      | | | | | | |   ||  ||    |     | |  |   |||     |  || || ||||||||||||||| |||||||||||||||||||||||||||||||| || || || |||||||| |||||||||||||| ||||| || || || ||||||||||
----taattaattaagaataaataaactctgcacaga-acacactatatgttaagctaggctgtgagatgctattctaagctgtcaaaattttccgtgtgaacagCTAAGTTTCGTGGACCTTGCTGGTTCTGAGAGGGTGAAAAAGTCCGGCTCAGCAGGAAAACAACTGAAAGAAGCTCAAAGCATCAATAAGTCTCTTTCTG

upper sequence: GRMZM2G423861_T02 (Zea mays), 3'ss of exon 20
lower sequence: GLYMA11G09480.1 (Glycine max), 3'ss of exon 22
-----------------------------------------tgtgaa-actattgcatcctaaacagtccttgggcttttgtag-agtttgtttcacat------tacacttacggggaagaattgacagtg--ttcctctgtttga---------------acagCTAAGTTTTGTGGACCTTGCTGGTTCTGAGAGGGTGAAAAAATCTGGTTCCGCAGGAAAGCAACTGAAAGAAGCACAAAGTATAAACAAATCTCTTTCTG
                                         | ||||   || |  | | ||  |   | ||    || ||||| | || |   || |       ||      || || |   | ||   |   ||  | |||| ||               |||| ||||||||||||| |||||||| || || || || ||||| ||||||||  |||| |  ||||| |||||||| |||||||| ||||||||  | || |
gtattattgtacattacttgtattttacctttgaatatcagtatgaatgttagtataccatattcttccttta---ttatgtagcaattcgaaacataagtattgtatgacctcgaggcaatgtggattttaactttttatgttggatttgtcatttgtcatacagTTAAGTTTTGTGGATCTTGCTGGCTCAGAAAGAGTAAAAAAGTCTGGTTCTTCAGGTAGTCAACTTAAAGAAGCTCAAAGTATCAACAAATCATTATCAG

upper sequence: GRMZM2G423861_T02 (Zea mays), 3'ss of exon 20
lower sequence: GLYMA09G32740.1 (Glycine max), 3'ss of exon 22
tgtgaaactattgcatc----ctaaacagtccttgggcttttgtagagtttgtttcacattacacttacggggaagaattgacagtgttcctctgtttgaacagCTAAGTTTTGTGGACCTTGCTGGTTCTGAGAGGGTGAAAAAATCTGGTTCCGCAGGAAAGCAACTGAAAGAAGCACAAAGTATAAACAAATCTCTTTCTG
   |||| | || | ||     ||| ||    |  ||    |  |  |||| ||   | | |  | |  |   |   |||     ||||    |   |   ||||| ||||||||||| ||||||||||| || || |||||||| || |||||  | || |  || || || ||||| ||||| || ||||| ||  | || |
--ggaaaatgtttcttcattgttaagcaacaatatggaacatcaattgtttcttgagcttgaggcatgtgcttacttatt--ttatgttggattcaatatgcagCTGAGTTTTGTGGATCTTGCTGGTTCAGAAAGAGTGAAAAAGTCAGGTTCTACTGGGAGTCAGCTTAAGGAAGCTCAAAGCATTAACAAGTCATTATCAG

upper sequence: GRMZM2G423861_T02 (Zea mays), 3'ss of exon 20
lower sequence: GLYMA16G21340.1 (Glycine max), 3'ss of exon 25
--tgtgaaactattgcatcctaaacagtccttgggcttttgtagagtttgtttcacattacacttacggggaagaattgaca-gtgttcctctgtttgaacagCTAAGTTTTGTGGACCTTGCTGGTTCTGAGAGGGTGAAAAAATCTGGTTCCGCAGGAAAGCAACTGAAAGAAGCACAAAGTATAAACAAATCTCTTTCTG
   |  ||| | || | || |    |  |       |     |  | |||||||   ||   ||   || |     ||      | ||    |   |   ||||||||||||||||| ||||||||||| || || |||||||| || |||||  | || |  || || || ||||| || || || ||||| ||  | || |
cagggaaaaatgtttcttcattgttaagcaacaatgtggaacattgattgtttc---ttgagctcgtggtgcgtgcttattttatcttggattcaatatgcagCTAAGTTTTGTGGATCTTGCTGGTTCAGAAAGAGTGAAAAAGTCAGGTTCTACCGGGAGTCAGCTTAAGGAAGCTCAGAGCATTAACAAGTCATTATCAG

upper sequence: GRMZM2G423861_T02 (Zea mays), 3'ss of exon 20
lower sequence: AT5G65930.2 (Arabidopsis thaliana), 3'ss of exon 19
tgtgaaactattgcatcctaaacagtccttgggcttttgtagagtttgtttcacattacacttacgggga-------agaattgacagtgttcctctgtt-tgaacagCTAAGTTTTGTGGACCTTGCTGGTTCTGAGAGGGTGAAAAAATCTGGTTCCGCAGGAAAGCAACTGAAAGAAGCACAAAGTATAAACAAATCTCTTTCTG
    | | ||||      | |   | |||    |  ||||  |     | |||| | |   |   ||          |  |||   | | ||  | |||| |   ||||| ||||||||||| ||||||||||||||||| || ||||| || || || || ||    ||||| |||||||| |||||||| |||||||| |||||||
----atattattagtcaatgatatgccct----ccattgttaaacccatatcacctgatcatggtggtatcttctacaatattctgaatttttgtttgttatttgcagCTGAGTTTTGTGGATCTTGCTGGTTCTGAGAGAGTTAAAAAGTCGGGCTCAGCTGGTTGTCAACTCAAAGAAGCTCAAAGTATCAACAAATCACTTTCTG

upper sequence: GRMZM2G423861_T02 (Zea mays), 3'ss of exon 20
lower sequence: Vv04s0044g02020.t01 (Vitis vinifera), 3'ss of exon 21
----tgtgaaactattgcatcctaaacagtcctt--gggctt--ttgtagagtttgtttcacattacacttacggggaagaattgacagtgttcctctgtttgaacagCTAAGTTTTGTGGACCTTGCTGGTTCTGAGAGGGTGAAAAAATCTGGTTCCGCAGGAAAGCAACTGAAAGAAGCACAAAGTATAAACAAATCTCTTTCTG
    ||||  |  || |  |   | |       |  ||||||  || | | | |  | |    ||    ||||  |  |   || | |      |||| | ||  ||||||||||||||||| ||||||||||| || |||||||| ||||| || ||  |||| || ||||| || ||||| ||||| || ||||| || ||||| |
aatctgtgttaacatggagtgtgagatgtcttgttggggcttacttattgtgataatgtttatttgtctttacatgacaattttaaaa------ctctatctg--cagCTAAGTTTTGTGGATCTTGCTGGTTCAGAAAGGGTGAAGAAATCAGGCTCTTCAGGTAATCAACTTAAGGAAGCTCAAAGCATCAACAAGTCACTTTCAG

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|67042488|gb|CO468743.1|CO468743
EST:     TCATTATTGAAAGTACAAATCTTCAAACCCAATCATATGCAAGAGGCAAG                         CTAAGTTTTGTGGACCTTGCTGGTTCTGAGAGGGTGAAAAAATCTGGTTCC
genomic: TCATTATTGAAAGTACAAATCTTCAAACCCAATCATATGCAAGAGGCAAGgtatggacag ... gtttgaacagCTAAGTTTTGTGGACCTTGCTGGTTCTGAGAGGGTGAAAAAATCTGGTTCC
EST: gi|211378041|gb|FL328240.1|FL328240
EST:     CATTATTGAAAGTACAAATCTTCAAACCCAATCATATGCAAGAGGCAAG                         CTAAGTTTTGTGGACCTTGCTGGTTCTGAGAGGGTGAAAAAATCTGGTTCC
genomic: CATTATTGAAAGTACAAATCTTCAAACCCAATCATATGCAAGAGGCAAGgtatggacag ... gtttgaacagCTAAGTTTTGTGGACCTTGCTGGTTCTGAGAGGGTGAAAAAATCTGGTTCC

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), 44 (downstream exon)
Score: 126

CGGAACTAATATGAATGATGAGAGTTCAAGGTCTCATTTAATTCTTTCAGTCATTATTGAAAGTACAAATCTTCAAACCCAATCATATGCAAGAGGCAAGgtatggacag ... gtttgaacagCTAAGTTTTGTGGACCTTGCTGGTTCTGAGAGGGTGAAAAAATCTGGTTCCGCAGGAAAGCAACTGAAAGAAGCACAAAGTATAAACAAATCTCTTTCTG


Block sizes: 44 (upstream exon), 44 (downstream exon)
Score: 14

CGGAACTAATATGAATGATGAGAGTTCAAGGTCTCATTTAATTCTTTCAGTCATTATTGAAAGTACAAATCTTCAAACCCAATCATATGCAAGAGGCAAGgtatggacag ... gtttgaacagCTAAGTTTTGTGGACCTTGCTGGTTCTGAGAGGGTGAAAAAATCTGGTTCCGCAGGAAAGCAACTGAAAGAAGCACAAAGTATAAACAAATCTCTTTCTG


Block sizes: 43 (upstream exon), 47 (downstream exon)
Score: 7

CGGAACTAATATGAATGATGAGAGTTCAAGGTCTCATTTAATTCTTTCAGTCATTATTGAAAGTACAAATCTTCAAACCCAATCATATGCAAGAGGCAAGgtatggacag ... gtttgaacagCTAAGTTTTGTGGACCTTGCTGGTTCTGAGAGGGTGAAAAAATCTGGTTCCGCAGGAAAGCAACTGAAAGAAGCACAAAGTATAAACAAATCTCTTTCTG


Block sizes: 49 (upstream exon), 44 (downstream exon)
Score: 55

CGGAACTAATATGAATGATGAGAGTTCAAGGTCTCATTTAATTCTTTCAGTCATTATTGAAAGTACAAATCTTCAAACCCAATCATATGCAAGAGGCAAGgtatggacag ... gtttgaacagCTAAGTTTTGTGGACCTTGCTGGTTCTGAGAGGGTGAAAAAATCTGGTTCCGCAGGAAAGCAACTGAAAGAAGCACAAAGTATAAACAAATCTCTTTCTG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttgtttcacattacacttacggggaagaattgacagtgttcctctgtttgaacagCTAAGTTTTGTGGACCTTGCTGGTTCTGAGAGGGTGAAAAAATCTGGTTCCGCAGGAAAGCAACTGAAAGAAGCACAAAGTATAAACAAATCTCTTTCTG
                                      ttcctctgttt  CT-rich tract
                        aagaatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tgtgaaactattgcatcctaaacagtccttgggcttttgtagagtttgtttcacattacacttacggggaagaattgacagtgttcctctgtttgaacagCTAAGTTTTGTGGACCTTGCTGGTTCTGAGAGGGTGAAAAAATCTGGTTCCGCAGGAAAGCAACTGAAAGAAGCACAAAGTATAAACAAATCTCTTTCTG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGCAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGC
- - - - - -tgcatcc
- - - - - - - - - - - - gtccttg
- - - - - - - - - - - - - - - - gcttttg
- - - - - - - - - - - - - - - - - - - - - - - tgtttca