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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaaccatgcatgcatcctggcaaacacgcagcagcagcatcgctcgctggaatggcagatctgtgaccagcattagccggcggtgcagGAGGAGGACAAGGTGAGGCTGGCGGCGGCGACTGGGCTGGACCCGAAGCAGATCAACAACTGGTTCATCAACCAGCGGAAGCGGCACTGGAAGCCGTCCG

Basic information

species Zea mays
transcript GRMZM2G094241_T01
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G094241_T01 (Zea mays), 3'ss of exon 4
lower sequence: LOC_Os05g03884.1 (Oryza sativa), 3'ss of exon 4
gtaaccatgcatgcat-cctggcaaacacgcagcagcagc-atcgctcgctggaatggcagatctgtgaccagcattagccggcggtgcagGAGGAGGACAAGGTGAGGCTGGCGGCGGCGACTGGGCTGGACCCGAAGCAGATCAACAACTGGTTCATCAACCAGCGGAAGCGGCACTGGAAGCCGTCCG
||||    ||    |  |||     |||| ||  |||  | | | | | |||   ||| |  |||||   |   |||   |       ||||| ||||| |||||||||||||| |||  |||||| || |||||||||||||||||||||||||||||||||||| ||||| ||||||||||||| || |
gtaatgtcgcgaaaacgccttttcgacacacaaaagcctctaacccacactgacctgggac-tctgtcttcca-attgatcttt--cacagGAAGAGGATAAGGTGAGGCTGGCCGCGATGACTGGCCTCGACCCGAAGCAGATCAACAACTGGTTCATCAACCAGAGGAAGAGGCACTGGAAGCCATCGG

upper sequence: GRMZM2G094241_T01 (Zea mays), 3'ss of exon 4
lower sequence: Vv14s0060g01180.t01 (Vitis vinifera), 3'ss of exon 4
-----gtaaccatgcatgcatcctggcaaacac-gcagcagcagca-tcgctcgctggaat-----ggcagatctgtgaccagcattagccggcggtgcagGAGGAGGACAAGGTGAGGCTGGCGGCGGCGACTGGGCTGGACCCGAAGCAGATCAACAACTGGTTCATCAACCAGCGGAAGCGGCACTGGAAGCCGTCCG
      | |   || |    |  |   ||   |    || |   || | | |  ||   ||     | ||  | | |||  || ||| |  |  | | ||||| || || ||  ||| |||  | | ||  ||||| || |||| ||||||||| |||||||||||||| |||||| |||||||||| ||||| || || |
aaaagttcatattggagttgtatttagaactgctatcgctgggacacttgtttactttcatttctggacacgtatctgaaaaggatt-gatgatgatacagGAAGATGAGAAATTGAAGCTATCAGAGGTTACTGGACTAGACCAGAAGCAGATTAACAACTGGTTCATAAACCAGAGGAAGCGGCATTGGAAACCATCAG

upper sequence: GRMZM2G094241_T01 (Zea mays), 3'ss of exon 4
lower sequence: PP1S235_27V6.1 (Physcomitrella patens), 3'ss of exon 6
--------gtaaccatgcatgcatcctggcaaacacgcagcagcagcatcgctcgctggaatggcagatctgtgaccagcattagccggcggtgcagGAGGAGGACAAGGTGAGGCTGGCGGCGGCGACT----GGGCTGGACCCGAAGCAGATCAACAACTGGTTCATCAACCAGCGGAAGCGGCACTGGAAGCCGTCCG-
         |||  |   || || | | | |||        |  |    ||||   ||   |     |  | | |||| |  |     ||  |  |    |  ||    |  |   |  | ||    |||    || ||  |||  ||||| || |||||||||||||||||  |||| ||||||||||||| || |   | 
aagttattttaaggagatat-caccatagaaaaacaattaaaataatgacgctgcttgtcttctagaagttctaaccaactgtcaagtgcactctacacagGAGATGGAGAAACAGTACCTGCAAAAACTCTGCGGTCTAAACCTAAAGCAAATTAACAACTGGTTCATCAATGAGCGCAAGCGGCACTGGA-GCTGCGAGG

upper sequence: GRMZM2G094241_T01 (Zea mays), 3'ss of exon 4
lower sequence: EFJ23803 (Selaginella moellendorffii), 3'ss of exon 4
---------------------------------------------------gtaacca-tgcatgcatcctggcaaacacgcagcagcagcatcgctcgctggaatggcagatctgtgaccagcattagccggcggtgcagGAGGAGGACAAGGTGAGGCTGGCGGCGGCGACTGGGCTGGACCCGAAGCAGATCAACAACTGGTTCATCAACCAGCGGAAGCGGCACTGGAAGCCGTCCG
                                                    |  | | ||   |   | ||||       |       |  ||  |  |     |      | ||  |   || |      || |  |||||| |  | |||  ||  || |||    | || ||||||||||| |||||||||||||||||||| || |||||||| |||||||||||||| |||   |
gtgagtacctttgtgttctttcttgttggcattctgtgtctctttctcgttatggctagtgggcgtgccatggctt-tgttccttctttgtgtccttttcatcgcttttttctttgacatttgcttcgttgtgctggacagGAGAACCAAAAGTCGAATCTCGCGCAATCCACCGGGCTGGACCCAAAGCAGATCAACAACTGGTTTATAAACCAGCGAAAGCGGCACTGGAATCCGCAGG

upper sequence: GRMZM2G094241_T01 (Zea mays), 3'ss of exon 4
lower sequence: EFJ21443 (Selaginella moellendorffii), 3'ss of exon 5
---------------------------------------------------gtaacca-tgcatgcatcctggcaaacacgcagcagcagcatcgctcgctggaatggcagatctgtgaccagcattagccggcggtgcagGAGGAGGACAAGGTGAGGCTGGCGGCGGCGACTGGGCTGGACCCGAAGCAGATCAACAACTGGTTCATCAACCAGCGGAAGCGGCACTGGAAGCCGTCCG
                                                    |  | | ||   |   | ||||       |       |  ||  |  |     |      | ||  |   || |      || |  |||||| |  | |||  ||  || |||    | || || |||||||| |||||||||||||||||||| || |||||||| |||||||||||||| ||    |
gtgagtacctttgtgttctttcttgttggcattccgtgtctctttctcgttatggctagtgggcgtgccatggctt-tgttccttctttgtgtccttttcattgcttttttctttgacatttgcttcgctgtgctggacagGAGAACCAAAAGTCGAATCTCGCGCAATCCACCGGCCTGGACCCAAAGCAGATCAACAACTGGTTTATAAACCAGCGAAAGCGGCACTGGAATCCACAGG

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|60339785|gb|DN206758.1|DN206758
EST:     CGGCGCTCATGGACTGGTGGAACACGCACTACCGCTGGCCGTACCCTACG                         GAGGAGGACAAGGTGAGGCTGGCGGCGGCGACTGGGCTGGACCCTAAGCAA
genomic: CGGCGCTCATGGACTGGTGGAACACGCACTACCGCTGGCCGTACCCTACGgtaaccatgc ... ggcggtgcagGAGGAGGACAAGGTGAGGCTGGCGGCGGCGACTGGGCTGGACCCGAAGCAG
EST: gi|60347276|gb|DN214249.1|DN214249
EST:     CGGCGCTCATGGACTGGTGGAACACGCACTACCGCTGGCCGTACCCTACG                         GAGGAGGACAAGGTGAGGCTGGCGGCGGCGACTGGGCTGGACCCTAAGCAA
genomic: CGGCGCTCATGGACTGGTGGAACACGCACTACCGCTGGCCGTACCCTACGgtaaccatgc ... ggcggtgcagGAGGAGGACAAGGTGAGGCTGGCGGCGGCGACTGGGCTGGACCCGAAGCAG
EST: gi|76020026|gb|DT947196.1|DT947196
EST:     CGGCGCTCATGGACTGGTGGAACACGCACTACCGCTGGCCGTACCCTACG                         GAGGAGGACAAGGTGAGGCTGGCGGCGGCGACTGGGCTGGACCCGAAGCAG
genomic: CGGCGCTCATGGACTGGTGGAACACGCACTACCGCTGGCCGTACCCTACGgtaaccatgc ... ggcggtgcagGAGGAGGACAAGGTGAGGCTGGCGGCGGCGACTGGGCTGGACCCGAAGCAG
EST: gi|60340163|gb|DN207136.1|DN207136
EST:     CGGCGCTCATGGACTGGTGGAACACGCACTACCGCTGGCCGTACCCTACG                         GAGGAGGACAAGGTGAGGCTGGCGGCGGCGACTGGGCTGGACCCGAAGCAG
genomic: CGGCGCTCATGGACTGGTGGAACACGCACTACCGCTGGCCGTACCCTACGgtaaccatgc ... ggcggtgcagGAGGAGGACAAGGTGAGGCTGGCGGCGGCGACTGGGCTGGACCCGAAGCAG
EST: gi|93284455|gb|EB676719.1|EB676719
EST:     CGGCGCTCATGGACTGGTGGAACACGCACTACCGCTGGCCGTACCCTACG                         GAGGAGGACAAGGTGAGGCTGGCGGCGGCGACTGGGCTGGACCCGAAGCAG
genomic: CGGCGCTCATGGACTGGTGGAACACGCACTACCGCTGGCCGTACCCTACGgtaaccatgc ... ggcggtgcagGAGGAGGACAAGGTGAGGCTGGCGGCGGCGACTGGGCTGGACCCGAAGCAG
EST: gi|113701815|gb|EE679319.1|EE679319
EST:     CGGCGCTCATGGACTGGTGGAACACGCACTACCGCTGGCCGTACCCTACG                         GAGGAGGACAAGGTGAGGCTGGCGGCGGCGACTGGGCTGGACCCGAAGCAG
genomic: CGGCGCTCATGGACTGGTGGAACACGCACTACCGCTGGCCGTACCCTACGgtaaccatgc ... ggcggtgcagGAGGAGGACAAGGTGAGGCTGGCGGCGGCGACTGGGCTGGACCCGAAGCAG
EST: gi|93284296|gb|EB676560.1|EB676560
EST:     CGGCGCTCATGGACTGGTGGAACACGCACTACCGCTGGCCGTACCCTACG                         GAGGAGGACAAGGTGAGGCTGGCGGCGGCGACTGGGCTGGACCCGAAGCAG
genomic: CGGCGCTCATGGACTGGTGGAACACGCACTACCGCTGGCCGTACCCTACGgtaaccatgc ... ggcggtgcagGAGGAGGACAAGGTGAGGCTGGCGGCGGCGACTGGGCTGGACCCGAAGCAG
EST: gi|32836955|gb|CD976633.1|CD976633
EST:     CGGCGCTCATGGACTGGTGGAACACGCACTACCGCTGGCCGTACCCTACG                         GAGGAGGACAAGGTGAGGCTGGCGGCGGCGACTGGGCTGGACCCGAAGCAG
genomic: CGGCGCTCATGGACTGGTGGAACACGCACTACCGCTGGCCGTACCCTACGgtaaccatgc ... ggcggtgcagGAGGAGGACAAGGTGAGGCTGGCGGCGGCGACTGGGCTGGACCCGAAGCAG
EST: gi|32837682|gb|CD977360.1|CD977360
EST:     CGGCGCTCATGGACTGGTGGAACACGCACTACCGCTGGCCGTACCCTACG                         GAGGAGGACAAGGTGAGGCCTGGCGGCGGCGACTGGGCTGGACCCGAAGCA
genomic: CGGCGCTCATGGACTGGTGGAACACGCACTACCGCTGGCCGTACCCTACGgtaaccatgc ... ggcggtgcagGAGGAGGACAAGGTGAGGC-TGGCGGCGGCGACTGGGCTGGACCCGAAGCA

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: 44

CGAGTTCCTGAAGAAGAGGAAGAAAGGGAAGCTGCCCAAGGACGCGCGGTCGGCGCTCATGGACTGGTGGAACACGCACTACCGCTGGCCGTACCCTACGgtaaccatgc ... ggcggtgcagGAGGAGGACAAGGTGAGGCTGGCGGCGGCGACTGGGCTGGACCCGAAGCAGATCAACAACTGGTTCATCAACCAGCGGAAGCGGCACTGGAAGCCGTCCG


Block sizes: 47 (upstream exon), 27 (downstream exon)
Score: 22

CGAGTTCCTGAAGAAGAGGAAGAAAGGGAAGCTGCCCAAGGACGCGCGGTCGGCGCTCATGGACTGGTGGAACACGCACTACCGCTGGCCGTACCCTACGgtaaccatgc ... ggcggtgcagGAGGAGGACAAGGTGAGGCTGGCGGCGGCGACTGGGCTGGACCCGAAGCAGATCAACAACTGGTTCATCAACCAGCGGAAGCGGCACTGGAAGCCGTCCG


Block sizes: 49 (upstream exon), 42 (downstream exon)
Score: 25

CGAGTTCCTGAAGAAGAGGAAGAAAGGGAAGCTGCCCAAGGACGCGCGGTCGGCGCTCATGGACTGGTGGAACACGCACTACCGCTGGCCGTACCCTACGgtaaccatgc ... ggcggtgcagGAGGAGGACAAGGTGAGGCTGGCGGCGGCGACTGGGCTGGACCCGAAGCAGATCAACAACTGGTTCATCAACCAGCGGAAGCGGCACTGGAAGCCGTCCG


Block sizes: 28 (upstream exon), 22 (downstream exon)
Score: 1

CGAGTTCCTGAAGAAGAGGAAGAAAGGGAAGCTGCCCAAGGACGCGCGGTCGGCGCTCATGGACTGGTGGAACACGCACTACCGCTGGCCGTACCCTACGgtaaccatgc ... ggcggtgcagGAGGAGGACAAGGTGAGGCTGGCGGCGGCGACTGGGCTGGACCCGAAGCAGATCAACAACTGGTTCATCAACCAGCGGAAGCGGCACTGGAAGCCGTCCG


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaaccatgcatgcatcctggcaaacacgcagcagcagcatcgctcgctggaatggcagatctgtgaccagcattagccggcggtgcagGAGGAGGACAAGGTGAGGCTGGCGGCGGCGACTGGGCTGGACCCGAAGCAGATCAACAACTGGTTCATCAACCAGCGGAAGCGGCACTGGAAGCCGTCCG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -CGGCGGCG