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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GGAGTTTTCCAAGAAGAAGAAGAAAGGGAAGCTCCCAAAGGAGGCCAGGCAGAAACTCCTCCACTGGTGGGAGCTGCACTACAAGTGGCCGTACCCTTCAgtaagatatactatctgatatctctcataccatacattaatgctcatatgtataaagaacaaacacaacgccatcgtccatgtcatgataagaatgataa...

Basic information

species Zea mays
transcript GRMZM2G028041_T01
intron # 4
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G028041_T01 (Zea mays), 5'ss of exon 4
lower sequence: LOC_Os07g03770.1 (Oryza sativa), 5'ss of exon 4
GGAGTTTTCCAAGAAGAAGAAGAAAGGGAAGCTCCCAAAGGAGGCCAGGCAGAAACTCCTCCACTGGTGGGAGCTGCACTACAAGTGGCCGTACCCTTCAgtaagat-atactatctgatatctctcataccatacattaatgctcatatgtataaagaacaaacacaacgccat---cgtccatgtcatgataagaatgataa--------------------------------------
 || ||||||||||| ||||||||||| ||||| || ||||||||||||||||| || || ||||||||||||||||||||||||||||| ||||| |||||||||| | ||   |  |  |  || |||  ||| | ||||   || |  ||   |   || ||| |   | |    | ||   ||   ||| |||   || |                                      
AGAATTTTCCAAGAAAAAGAAGAAAGGAAAGCTGCCTAAGGAGGCCAGGCAGAAGCTGCTTCACTGGTGGGAGCTGCACTACAAGTGGCCTTACCCCTCAgtaagattacacatacaaaattacctgataatatatagtaattgccacaattacctaatgcatacatagttctacaaacatcttagttcagatcagatgcatcatcacattgttactaactttgcaccaatgggatgagtag

upper sequence: GRMZM2G028041_T01 (Zea mays), 5'ss of exon 4
lower sequence: Vv18s0001g08380.t01 (Vitis vinifera), 5'ss of exon 4
GGAGTTTTCCAAGAAGAAGAAGAAAGGGAAGCTCCCAAAGGAGGCCAGGCAGAAACTCCTCCACTGGTGGGAGCTGCACTACAAGTGGCCGTACCCTTCAgtaag-atatactatctgatatctctcatac-------catacattaatgctcatatgtataaagaac---aaacacaacgccatcgtccatgtcatgataagaatgataa--------------------------------------------------------------
 ||| |||||||||| |||||||||||||| || || || || ||||||||||| || ||| | ||||||||| | |||||||| ||||| ||||| |||||| | |||| || | |||  | | || |||       || ||  | |   | || | || | | ||    |||    |    |   |  |||| |  | || |||  | |                                                              
AGAGCTTTCCAAGAAAAAGAAGAAAGGGAAACTACCCAAAGACGCCAGGCAGAAGCTACTCAATTGGTGGGAGTTACACTACAAATGGCCATACCCCTCAgtatgcatatcctctttgacctgtatcctacacttggtcaaactgttagaatgatctttacataaaattctaaattggaacaaagtatatatgttacta-aaaaatatttattgtttttcttgttccttgttcttgagatattaatgcagtgacacttctgatgatttcacag
















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|71433443|gb|DR814493.1|DR814493
EST:     AAGTGGCCGTACCCTTCA                         GAGACGGAGAAGATTGCGCTCGCAGAATCAACGGGCCTAGACCAGAAGCAG
genomic: AAGTGGCCGTACCCTTCAgtaagatata ... gttcgagcagGAGACGGAGAAGATTGCGCTCGCAGAATCAACGGGCCTAGACCAGAAGCAG
EST: gi|211105912|gb|FK984438.1|FK984438
EST:     AGAAACTCCTCCACTGGTGGGAGCTGCACTACAAGTGGCCGTACCCTTCA                         GAGACGGAGAAGATTGCGCTCGCAGAATCAACGGGCCTAGACCAGAAGCAG
genomic: AGAAACTCCTCCACTGGTGGGAGCTGCACTACAAGTGGCCGTACCCTTCAgtaagatata ... gttcgagcagGAGACGGAGAAGATTGCGCTCGCAGAATCAACGGGCCTAGACCAGAAGCAG
EST: gi|60393930|gb|DN226800.1|DN226800
EST:     AGAAACTCCTCCACTGGTGGGAGCTGCACTACAAGTGGCCGTACCCTTCA                         GAGACGGAGAAGATTGCGCTCGCAGAATCAACGGGCCTAGACCAGAAGCAG
genomic: AGAAACTCCTCCACTGGTGGGAGCTGCACTACAAGTGGCCGTACCCTTCAgtaagatata ... gttcgagcagGAGACGGAGAAGATTGCGCTCGCAGAATCAACGGGCCTAGACCAGAAGCAG
EST: gi|211255945|gb|FL455104.1|FL455104
EST:     AGAAACTCCTCCACTGGTGGGAGCTGCACTACAAGTGGCCGTACCCTTCA                         GAGACGGAGAAGATTGCGCTCGCAGAATCAACGGGCCTAGACCAGAAGCAG
genomic: AGAAACTCCTCCACTGGTGGGAGCTGCACTACAAGTGGCCGTACCCTTCAgtaagatata ... gttcgagcagGAGACGGAGAAGATTGCGCTCGCAGAATCAACGGGCCTAGACCAGAAGCAG
EST: gi|50329611|gb|CO524737.1|CO524737
EST:     AGAAACTCCTCCACTGGTGGGAGCTGCACTACAAGTGGCCGTACCCTTCA                         GAGACGGAGAAGATTGCGCTCGCAGAATCAACGGGCCTAGACCAGAAGCAG
genomic: AGAAACTCCTCCACTGGTGGGAGCTGCACTACAAGTGGCCGTACCCTTCAgtaagatata ... gttcgagcagGAGACGGAGAAGATTGCGCTCGCAGAATCAACGGGCCTAGACCAGAAGCAG
EST: gi|60355037|gb|DN222010.1|DN222010
EST:     AGAAACTCCTCCACTGGTGGGAGCTGCACTACAAGTGGCCGTACCCTTCA                         GAGACGGAGAAGATTGCGCTCGCAGAATCAACGGGCCTAGACCAGAAGCAG
genomic: AGAAACTCCTCCACTGGTGGGAGCTGCACTACAAGTGGCCGTACCCTTCAgtaagatata ... gttcgagcagGAGACGGAGAAGATTGCGCTCGCAGAATCAACGGGCCTAGACCAGAAGCAG
EST: gi|101396808|gb|EB820330.1|EB820330
EST:     AGAAACTCCTCCACTGGTGGGAGCTGCACTACAAGTGGCCGTACCCTTCA                         GAGACGGAGAAGATTGCGCTCGCAGAATCAACGGGCCTAGACCAGAAGCAG
genomic: AGAAACTCCTCCACTGGTGGGAGCTGCACTACAAGTGGCCGTACCCTTCAgtaagatata ... gttcgagcagGAGACGGAGAAGATTGCGCTCGCAGAATCAACGGGCCTAGACCAGAAGCAG
EST: gi|76286051|gb|DV025619.1|DV025619
EST:     AGAAACTCCTCCACTGGTGGGAGCTGCACTACAAGTGGCCGTACCCTTCA                         GAGACGGAGAAGATTGCGCTCGCAGAATCAACGGGCCTAGACCAGAAGCAG
genomic: AGAAACTCCTCCACTGGTGGGAGCTGCACTACAAGTGGCCGTACCCTTCAgtaagatata ... gttcgagcagGAGACGGAGAAGATTGCGCTCGCAGAATCAACGGGCCTAGACCAGAAGCAG
EST: gi|101389983|gb|EB816923.1|EB816923
EST:     AGAAACTCCTCCACTGGTGGGAGCTGCACTACAAGTGGCCGTACCCTTCA                         GAGACGGAGAAGATTGCGCTCGCAGAATCAACGGGCCTAGACCAGAAGCAG
genomic: AGAAACTCCTCCACTGGTGGGAGCTGCACTACAAGTGGCCGTACCCTTCAgtaagatata ... gttcgagcagGAGACGGAGAAGATTGCGCTCGCAGAATCAACGGGCCTAGACCAGAAGCAG
EST: gi|76931671|gb|DV172798.1|DV172798
EST:     AGAAACTCCTCCACTGGTGGGAGCTGCACTACAAGTGGCCGTACCCTTCA                         GAGACGGAGAAGATTGCGCTCGCAGAATCAACGGGCCTAGACCAGAAGCAG
genomic: AGAAACTCCTCCACTGGTGGGAGCTGCACTACAAGTGGCCGTACCCTTCAgtaagatata ... gttcgagcagGAGACGGAGAAGATTGCGCTCGCAGAATCAACGGGCCTAGACCAGAAGCAG
EST: gi|60345527|gb|DN212500.1|DN212500
EST:     AGAAACTCCTCCACTGGTGGGAGCTGCACTACAAGTGGCCGTACCCTTCA                         GAGACGGAGAAGATTGCGCTCGCAGAATCAACGGGCCTAGACCAGAAGCAG
genomic: AGAAACTCCTCCACTGGTGGGAGCTGCACTACAAGTGGCCGTACCCTTCAgtaagatata ... gttcgagcagGAGACGGAGAAGATTGCGCTCGCAGAATCAACGGGCCTAGACCAGAAGCAG
EST: gi|211220404|gb|FL437615.1|FL437615
EST:     AGAAACTCCTCCACTGGTGGGAGCTGCACTACAAGTGGCCGTACCCTTCA                         GAGACGGAGAAGATTGCGCTCGCAGAATCAACGGGCCTAGACCAGAAGCAG
genomic: AGAAACTCCTCCACTGGTGGGAGCTGCACTACAAGTGGCCGTACCCTTCAgtaagatata ... gttcgagcagGAGACGGAGAAGATTGCGCTCGCAGAATCAACGGGCCTAGACCAGAAGCAG
EST: gi|78073693|gb|DV502127.1|DV502127
EST:     AGAAACTCCTCCACTGGTGGGAGCTGCACTACAAGTGGCCGTACCCTTCA                         GAGACGGAGAAGATTGCGCTCGCAGAATCAACGGGCCTAGACCAGAAGCAG
genomic: AGAAACTCCTCCACTGGTGGGAGCTGCACTACAAGTGGCCGTACCCTTCAgtaagatata ... gttcgagcagGAGACGGAGAAGATTGCGCTCGCAGAATCAACGGGCCTAGACCAGAAGCAG
EST: gi|31910083|gb|CD651246.1|CD651246
EST:     AGAAACTCCTCCACTGGTGGGAGCTGCACTACAAGTGGCCGTACCCTTCA                         GAGACGGAGAAGATTGCGCTCGCAGAATCAACGGGCCTAGACCAGAAGCAG
genomic: AGAAACTCCTCCACTGGTGGGAGCTGCACTACAAGTGGCCGTACCCTTCAgtaagatata ... gttcgagcagGAGACGGAGAAGATTGCGCTCGCAGAATCAACGGGCCTAGACCAGAAGCAG
EST: gi|93013896|gb|EB639416.1|EB639416
EST:     GGGAGCTGCACTACAAGTGGCCGTACCCTTCA                         GAGACGGAGAAGATTGCGCTCGCAGAATCAACGGGCCTAGACCAGAAGCAG
genomic: GGGAGCTGCACTACAAGTGGCCGTACCCTTCAgtaagatata ... gttcgagcagGAGACGGAGAAGATTGCGCTCGCAGAATCAACGGGCCTAGACCAGAAGCAG
EST: gi|33098196|gb|CF058156.1|CF058156
EST:     AGAAACTCCTCCACTGGTGGGAGCTGCACTACAAGTGGCCGTACCCTTCA                         GAGACGGAGAAGATTGCGCTCGCAGAATCAACGGGCCTAGACCAGAAGCAG
genomic: AGAAACTCCTCCACTGGTGGGAGCTGCACTACAAGTGGCCGTACCCTTCAgtaagatata ... gttcgagcagGAGACGGAGAAGATTGCGCTCGCAGAATCAACGGGCCTAGACCAGAAGCAG
EST: gi|29544802|gb|CB605410.1|CB605410
EST:     AGAAACTCCTCCACTGGTGGGAGCTGCACTACAAGTGGCCGTACCCTTCA                         GAGACGGAGAAGATTGCGCTCGCAGAATCAACGGGCCTAGACCAGAAGCAG
genomic: AGAAACTCCTCCACTGGTGGGAGCTGCACTACAAGTGGCCGTACCCTTCAgtaagatata ... gttcgagcagGAGACGGAGAAGATTGCGCTCGCAGAATCAACGGGCCTAGACCAGAAGCAG
EST: gi|28873323|gb|CB329327.1|CB329327
EST:     AGAAACTCCTCCACTGGTGGGAGCTGCACTACAAGTGGCCGTACCCTTCA                         GAGACGGAGAAGATTGCGCTCGCAGAATCAACGGGCCTAGACCAGAAGCAG
genomic: AGAAACTCCTCCACTGGTGGGAGCTGCACTACAAGTGGCCGTACCCTTCAgtaagatata ... gttcgagcagGAGACGGAGAAGATTGCGCTCGCAGAATCAACGGGCCTAGACCAGAAGCAG
EST: gi|91052590|gb|EB163008.1|EB163008
EST:     AGAAACTCCTCCACTGGTGGGAGCTGCACTACAAGTGGCCGTACCCTTCA                         GAGACGGAGAAGATTGCGCTCGCAGAATCAACGGGCCTAGACCAGAAGCAG
genomic: AGAAACTCCTCCACTGGTGGGAGCTGCACTACAAGTGGCCGTACCCTTCAgtaagatata ... gttcgagcagGAGACGGAGAAGATTGCGCTCGCAGAATCAACGGGCCTAGACCAGAAGCAG
EST: gi|60341856|gb|DN208829.1|DN208829
EST:     AGAAACTCCTCCACTGGTGGGAGCTGCACTACAAGTGGCCGTACCCTTCA                         GAGACGGAGAAGATTGCGCTCGCAGAATCAACGGGCCTAGACCAGAAGCAG
genomic: AGAAACTCCTCCACTGGTGGGAGCTGCACTACAAGTGGCCGTACCCTTCAgtaagatata ... gttcgagcagGAGACGGAGAAGATTGCGCTCGCAGAATCAACGGGCCTAGACCAGAAGCAG
EST: gi|149100768|gb|EE186862.2|EE186862
EST:     AGAAACTCCTCCACTGGTGGGAGCTGCACTACAAGTGGCCGTACCCTTCA                         GAGACGGAGAAGATTGCGCTCGCAGAATCAACGGGCCTAGACCAGAAGCAG
genomic: AGAAACTCCTCCACTGGTGGGAGCTGCACTACAAGTGGCCGTACCCTTCAgtaagatata ... gttcgagcagGAGACGGAGAAGATTGCGCTCGCAGAATCAACGGGCCTAGACCAGAAGCAG
EST: gi|60339748|gb|DN206721.1|DN206721
EST:     AGAAACTCCTCCACTGGTGGGAGCTGCACTACAAGTGGCCGTACCCTTCA                         GAGACGGAGAAGATTGCGCTCGCAGAATCAACGGGCCTAGACCAGAAGCAG
genomic: AGAAACTCCTCCACTGGTGGGAGCTGCACTACAAGTGGCCGTACCCTTCAgtaagatata ... gttcgagcagGAGACGGAGAAGATTGCGCTCGCAGAATCAACGGGCCTAGACCAGAAGCAG
EST: gi|18661474|gb|BM501416.1|BM501416
EST:     AGAAACTCCTCCACTGGTGGGAGCTGCACTACAAGTGGCCGTACCCTTCA                         GAGACGGAGAAGATTGCGCTCGCAGAATCAACGGGCCTAGACCAGAAGCAG
genomic: AGAAACTCCTCCACTGGTGGGAGCTGCACTACAAGTGGCCGTACCCTTCAgtaagatata ... gttcgagcagGAGACGGAGAAGATTGCGCTCGCAGAATCAACGGGCCTAGACCAGAAGCAG
EST: gi|93013895|gb|EB639415.1|EB639415
EST:     GGGAGCTGCACTACAAGTGGCCGTACCCTTCA                         GAGACGGAGAAGATTGCGGCTCGCAGAATCAACGGGCCTAGACCAGAAGCA
genomic: GGGAGCTGCACTACAAGTGGCCGTACCCTTCAgtaagatata ... gttcgagcagGAGACGGAGAAGATTGC-GCTCGCAGAATCAACGGGCCTAGACCAGAAGCA
EST: gi|33095633|gb|CF055627.1|CF055627
EST:     AGAAACTCCTCCACTGGTGGGAGCTGCACTACAAGTGGCCGTACCCTTCA                         GAGACGGAGAAGATTGCGCTCGCAGAATCAACGGGCCTAGACCAGAAGCAG
genomic: AGAAACTCCTCCACTGGTGGGAGCTGCACTACAAGTGGCCGTACCCTTCAgtaagatata ... gttcgagcagGAGACGGAGAAGATTGCGCTCGCAGAATCAACGGGCCTAGACCAGAAGCAG
EST: gi|60395483|gb|DN228353.1|DN228353
EST:     AGAAACTCCTCCACTGGTGGGAGCTGCACTACAAGTGGCCGTACCCTTCA                         GAGACGGAGAAGATTGCGCTCGCAGAATCAACGGGCCTAGACCAGAAGCAG
genomic: AGAAACTCCTCCACTGGTGGGAGCTGCACTACAAGTGGCCGTACCCTTCAgtaagatata ... gttcgagcagGAGACGGAGAAGATTGCGCTCGCAGAATCAACGGGCCTAGACCAGAAGCAG
EST: gi|71763226|gb|DR961163.1|DR961163
EST:     AGAAACTCCTCCACTGGTGGGAGCTGCACTACAAGTGGCCGTACCCTTCA                         GAGACGGAGAAGATTGCGCTCGCAGAATCAACGGGCCTAGACCAGAAGCAG
genomic: AGAAACTCCTCCACTGGTGGGAGCTGCACTACAAGTGGCCGTACCCTTCAgtaagatata ... gttcgagcagGAGACGGAGAAGATTGCGCTCGCAGAATCAACGGGCCTAGACCAGAAGCAG
EST: gi|78075576|gb|DV504010.1|DV504010
EST:     AGAAACTCCTCCACTGGTGGGAGCTGCACTACAAGTGGCCGTACCCTTCA                         GAGACGGAGAAGATTGCGCTCGCAGAATCAACGGGCCTAGACCAGAAGCAG
genomic: AGAAACTCCTCCACTGGTGGGAGCTGCACTACAAGTGGCCGTACCCTTCAgtaagatata ... gttcgagcagGAGACGGAGAAGATTGCGCTCGCAGAATCAACGGGCCTAGACCAGAAGCAG
EST: gi|101395432|gb|EB819644.1|EB819644
EST:     AGAAACTCCTCCACTGGTGGGAGCTGCACTCCAAGTGGCCGTACCCTTCA                         GAGACGGAGAAGATTGCGCTCGCAGAATCAACGGGCCTAGACCAGAAGCAG
genomic: AGAAACTCCTCCACTGGTGGGAGCTGCACTACAAGTGGCCGTACCCTTCAgtaagatata ... gttcgagcagGAGACGGAGAAGATTGCGCTCGCAGAATCAACGGGCCTAGACCAGAAGCAG
EST: gi|33096939|gb|CF056899.1|CF056899
EST:     AGAAACTCCTCCACTGGTGGGAGCTGCACTACAAGTGGCCGTACCCTTCA                         GAGACGGAGAAGATTGCGCTCGCAGAATCATCGGGCCTAGACCAGAAGCAG
genomic: AGAAACTCCTCCACTGGTGGGAGCTGCACTACAAGTGGCCGTACCCTTCAgtaagatata ... gttcgagcagGAGACGGAGAAGATTGCGCTCGCAGAATCAACGGGCCTAGACCAGAAGCAG

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: 305

GGAGTTTTCCAAGAAGAAGAAGAAAGGGAAGCTCCCAAAGGAGGCCAGGCAGAAACTCCTCCACTGGTGGGAGCTGCACTACAAGTGGCCGTACCCTTCAgtaagatata ... gttcgagcagGAGACGGAGAAGATTGCGCTCGCAGAATCAACGGGCCTAGACCAGAAGCAGATCAACAACTGGTTCATCAACCAGAGGAAACGGCACTGGAAGCCATCGG


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 70

GGAGTTTTCCAAGAAGAAGAAGAAAGGGAAGCTCCCAAAGGAGGCCAGGCAGAAACTCCTCCACTGGTGGGAGCTGCACTACAAGTGGCCGTACCCTTCAgtaagatata ... gttcgagcagGAGACGGAGAAGATTGCGCTCGCAGAATCAACGGGCCTAGACCAGAAGCAGATCAACAACTGGTTCATCAACCAGAGGAAACGGCACTGGAAGCCATCGG


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 58

GGAGTTTTCCAAGAAGAAGAAGAAAGGGAAGCTCCCAAAGGAGGCCAGGCAGAAACTCCTCCACTGGTGGGAGCTGCACTACAAGTGGCCGTACCCTTCAgtaagatata ... gttcgagcagGAGACGGAGAAGATTGCGCTCGCAGAATCAACGGGCCTAGACCAGAAGCAGATCAACAACTGGTTCATCAACCAGAGGAAACGGCACTGGAAGCCATCGG


Block sizes: 49 (upstream exon), 45 (downstream exon)
Score: 7

GGAGTTTTCCAAGAAGAAGAAGAAAGGGAAGCTCCCAAAGGAGGCCAGGCAGAAACTCCTCCACTGGTGGGAGCTGCACTACAAGTGGCCGTACCCTTCAgtaagatata ... gttcgagcagGAGACGGAGAAGATTGCGCTCGCAGAATCAACGGGCCTAGACCAGAAGCAGATCAACAACTGGTTCATCAACCAGAGGAAACGGCACTGGAAGCCATCGG


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GGAGTTTTCCAAGAAGAAGAAGAAAGGGAAGCTCCCAAAGGAGGCCAGGCAGAAACTCCTCCACTGGTGGGAGCTGCACTACAAGTGGCCGTACCCTTCAgtaagatatactatctgatatctctcataccatacattaatgctcatatgtataaagaacaaacacaacgccatcgtccatgtcatgataagaatgataa

- - - - - - - - - - - - - - - - - - - - - - - - - - -  CTCCTC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGTGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - aagaacaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - gataagaa