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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtctgttatctggcagccattagttttcgttggctcccagaaattgtctagcaactcttattttgctacataatgatgattgtagGTGGATAGAGCCAATGCAGATTTGAAGAATACCAACGTGAGACTGAAGGAGACTGTTCTTCAA

Basic information

species Zea mays
transcript GRMZM2G057251_T01
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G057251_T01 (Zea mays), 3'ss of exon 6
lower sequence: LOC_Os05g48020.1 (Oryza sativa), 3'ss of exon 6
gtctgttatctggcagccattagttt-tcgttggctcccagaaattgtctagcaactcttattttgct-----------------acataatgatgattgtagGTGGATAGAGCCAATGCAGATTTGAAGAATACCAACGTGAGACTGAAGGAGACTGTTCTTCAA
||  ||| ||    ||||||   ||  || |  ||        | | || |||||  |||| |||  |                    || |||||| |||||||||||||||||||  |||||||||||||||||||||| ||||| || ||||| |||||||| 
gttggttctccaatagccatggattcctcttctgcaattgtgcaatatccagcaatgcttagtttatttatctcttatttatatggtgtactgatgaatgtagGTGGATAGAGCCAACACAGATTTGAAGAATACCAACGTCAGACTAAAAGAGACCGTTCTTCAG
















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|166655401|gb|EG113788.1|EG113788
EST:     GAATTGGACAGACAAGTCCCTCTGATGGACGAAATGGATGATAAG                         GTGGATAGAGCCAATGCAG
genomic: GAATTGGACAGACAAGTCCCTCTGATGGACGAAATGGATGATAAGgtctgttatc ... atgattgtagGTGGATAGAGCCAATGCAG
EST: gi|74237329|gb|DT645243.1|DT645243
EST:     GAATTGGACAGACAAGTCCCTCTGATGGACGAAATGGATGATAAG                         GTGGATAGAGCCCATGCAGATTTGAAGATTACCAACGTGAGACTGAAGGAG
genomic: GAATTGGACAGACAAGTCCCTCTGATGGACGAAATGGATGATAAGgtctgttatc ... atgattgtagGTGGATAGAGCCAATGCAGATTTGAAGAATACCAACGTGAGACTGAAGGAG
EST: gi|60400857|gb|DN233664.1|DN233664
EST:     GAATTGGACAGACAAGTCCCTCTGATGGACGAAATGGATGATAAG                         GTGGATAGAGCCAATGCAGATTTGAAGAATACCAACGTGAGACTGAAGGAG
genomic: GAATTGGACAGACAAGTCCCTCTGATGGACGAAATGGATGATAAGgtctgttatc ... atgattgtagGTGGATAGAGCCAATGCAGATTTGAAGAATACCAACGTGAGACTGAAGGAG
EST: gi|71770367|gb|DR968304.1|DR968304
EST:     GAATTGGACAGACAAGTCCCTCTGATGGACGAAATGGATGATAGG                         GTGGATAGAGCCAATGCAGATTTGAAGAATACCAACGTGAGACTGAAGGAG
genomic: GAATTGGACAGACAAGTCCCTCTGATGGACGAAATGGATGATAAGgtctgttatc ... atgattgtagGTGGATAGAGCCAATGCAGATTTGAAGAATACCAACGTGAGACTGAAGGAG
EST: gi|60338253|gb|DN205226.1|DN205226
EST:     GAATTGGACAGACAAGTCCCTCTGATGGACGAAATGGATGATAAG                         GTGGATAGAGCCAATGCAGATTTGAAGAATACCAACGTGAGACTGAAGGAG
genomic: GAATTGGACAGACAAGTCCCTCTGATGGACGAAATGGATGATAAGgtctgttatc ... atgattgtagGTGGATAGAGCCAATGCAGATTTGAAGAATACCAACGTGAGACTGAAGGAG
EST: gi|78076770|gb|DV505204.1|DV505204
EST:     GAATTGGACAGACAAGTCCCTTTGATGGACGAAATGGATGATAAG                         GTGGATAGAGCCAATGCAGATTTGAAGAATACCAACGTGAGACTGAAGGAG
genomic: GAATTGGACAGACAAGTCCCTCTGATGGACGAAATGGATGATAAGgtctgttatc ... atgattgtagGTGGATAGAGCCAATGCAGATTTGAAGAATACCAACGTGAGACTGAAGGAG
EST: gi|76018601|gb|DT945771.1|DT945771
EST:     GAATTGGACAGACAAGTCCCTCTGATGGACGAAATGAATGATAAG                         GTGGATAGAGCCAATGCA
genomic: GAATTGGACAGACAAGTCCCTCTGATGGACGAAATGGATGATAAGgtctgttatc ... atgattgtagGTGGATAGAGCCAATGCA
EST: gi|78074902|gb|DV503336.1|DV503336
EST:     GAATTGGACAGACAAGTCCCTCTGATGGACGAAATGGATGATAAG                         GTGGATAGAGCCAATGCAGATTTGAAGAATACCAACGTGAGACTGAAGGAG
genomic: GAATTGGACAGACAAGTCCCTCTGATGGACGAAATGGATGATAAGgtctgttatc ... atgattgtagGTGGATAGAGCCAATGCAGATTTGAAGAATACCAACGTGAGACTGAAGGAG
EST: gi|91869751|gb|EB400522.1|EB400522
EST:     GAATTGGACAGACAAGTCCCTCTGATGGACGAAATGGATGATAAG                         GTGGATAGAGCCAATGCAGATTTGAAGAATACCAACGTGAGACTGAAGGAG
genomic: GAATTGGACAGACAAGTCCCTCTGATGGACGAAATGGATGATAAGgtctgttatc ... atgattgtagGTGGATAGAGCCAATGCAGATTTGAAGAATACCAACGTGAGACTGAAGGAG
EST: gi|78076771|gb|DV505205.1|DV505205
EST:     GAATTGGACAGACAAGTCCCTCTGATGGACGAAATGGATGATAAG                         GTGGATAGAGCCAATGCAGATTTGAAGAATACCAACGTGAGACTGAA
genomic: GAATTGGACAGACAAGTCCCTCTGATGGACGAAATGGATGATAAGgtctgttatc ... atgattgtagGTGGATAGAGCCAATGCAGATTTGAAGAATACCAACGTGAGACTGAA
EST: gi|60397948|gb|DN230764.1|DN230764
EST:     GAATTGGACAGACAAGTCCCTCTGATGGACGAAATGGATGATAAG                         GTGGATAGAGCCAATGCAGATTTGAAGAATACCAACGTGAGACTGAAGGAG
genomic: GAATTGGACAGACAAGTCCCTCTGATGGACGAAATGGATGATAAGgtctgttatc ... atgattgtagGTGGATAGAGCCAATGCAGATTTGAAGAATACCAACGTGAGACTGAAGGAG
EST: gi|211444699|gb|FL108662.1|FL108662
EST:     GAATTGGACAGACAAGTCCCTCTGATGGACGAAATGGATGATAAG                         GTGGATAGAGCCAATGCAGATTTGAAGAATACCAACGTGAGACTGAAGGAG
genomic: GAATTGGACAGACAAGTCCCTCTGATGGACGAAATGGATGATAAGgtctgttatc ... atgattgtagGTGGATAGAGCCAATGCAGATTTGAAGAATACCAACGTGAGACTGAAGGAG
EST: gi|60400044|gb|DN232851.1|DN232851
EST:     GAATTGGACAGACAAGTCCCTCTGATGGACGAAATGGATGATAAG                         GTGGATAGAGCCAATGCAGATTTGAAGAATACCAACGTGAGACTGAAGGAG
genomic: GAATTGGACAGACAAGTCCCTCTGATGGACGAAATGGATGATAAGgtctgttatc ... atgattgtagGTGGATAGAGCCAATGCAGATTTGAAGAATACCAACGTGAGACTGAAGGAG
EST: gi|74237328|gb|DT645242.1|DT645242
EST:     GAATTGGACAGACAAGTCCCTCTGATGGACGAAATGGATGATAAG                         GTGGATAGAGCCAATGCAGATTTGAAGAATACCAACGTGAGACTGAAGGAG
genomic: GAATTGGACAGACAAGTCCCTCTGATGGACGAAATGGATGATAAGgtctgttatc ... atgattgtagGTGGATAGAGCCAATGCAGATTTGAAGAATACCAACGTGAGACTGAAGGAG
EST: gi|71299507|gb|DR785763.1|DR785763
EST:     GAATTGGACAGACAAGTCCCTCTGATGGACGAAATGGATGATAAG                         GTGGATAGAGCCAATGCAGATTTGAAGAATACCAACGTGAGACTGAAGGAG
genomic: GAATTGGACAGACAAGTCCCTCTGATGGACGAAATGGATGATAAGgtctgttatc ... atgattgtagGTGGATAGAGCCAATGCAGATTTGAAGAATACCAACGTGAGACTGAAGGAG
EST: gi|76018600|gb|DT945770.1|DT945770
EST:     GAATTGGACAGACAAGTCCCTCTGATGGACGAAATGGATGATAAG                         GTGGATAGAGCCAATGCAGATTTGAAGAATACCAACGTGAGACTGAAGGAG
genomic: GAATTGGACAGACAAGTCCCTCTGATGGACGAAATGGATGATAAGgtctgttatc ... atgattgtagGTGGATAGAGCCAATGCAGATTTGAAGAATACCAACGTGAGACTGAAGGAG
EST: gi|78082804|gb|DV511197.1|DV511197
EST:     GAATTGGACAGACAAGTCCCTCTGATGGACGAAATGGATGATAAG                         GTGGATAGAGCCAATGCAGATTTGAAGAATACCAACGTGAGACTGAAGGAG
genomic: GAATTGGACAGACAAGTCCCTCTGATGGACGAAATGGATGATAAGgtctgttatc ... atgattgtagGTGGATAGAGCCAATGCAGATTTGAAGAATACCAACGTGAGACTGAAGGAG
EST: gi|32857817|gb|CD997498.1|CD997498
EST:     GAATTGGACAGACAAGTCCCTCTGATGGACGAAATGGCTGATAAG                         GTGGATAGAGCCAATGCAGATTTGAAGAACACCAACGTGAGACTGAAGGAG
genomic: GAATTGGACAGACAAGTCCCTCTGATGGACGAAATGGATGATAAGgtctgttatc ... atgattgtagGTGGATAGAGCCAATGCAGATTTGAAGAATACCAACGTGAGACTGAAGGAG
EST: gi|78086622|gb|DV515015.1|DV515015
EST:     GAATTGGACAGACAAGTCCCTCTGATGGACGAAATGGATGATAAG                         GTGGATAGAGCCAATGCAGATTTGAAGAATACCAACGTGAGACTGAAGGAG
genomic: GAATTGGACAGACAAGTCCCTCTGATGGACGAAATGGATGATAAGgtctgttatc ... atgattgtagGTGGATAGAGCCAATGCAGATTTGAAGAATACCAACGTGAGACTGAAGGAG
EST: gi|74235878|gb|DT643792.1|DT643792
EST:     GAATTGGACAGACAAGTCCCTCTGATGGACGAAATGGATGATAAG                         GTGGATAGAGCCAATGCAGATTTGAAGAATAC
genomic: GAATTGGACAGACAAGTCCCTCTGATGGACGAAATGGATGATAAGgtctgttatc ... atgattgtagGTGGATAGAGCCAATGCAGATTTGAAGAATAC
EST: gi|148932647|gb|EC876561.2|EC876561
EST:     GAATTGGACAGACCAGTCCCTCTGATGGACGAAATGCATGATAAG                         GTGGATAGAGCCAATGCAGATTTGAAGAATACCAACGTGAGACT
genomic: GAATTGGACAGACAAGTCCCTCTGATGGACGAAATGGATGATAAGgtctgttatc ... atgattgtagGTGGATAGAGCCAATGCAGATTTGAAGAATACCAACGTGAGACT
EST: gi|76281470|gb|DV021038.1|DV021038
EST:     GAATTGGACAGACAAGTCCCTCTGATGGACGAAATGGATGATAAG                         GTGGATAGAGCCAATGCAGATTTGAAGAATACCAACGTGAGACTGAAGGAG
genomic: GAATTGGACAGACAAGTCCCTCTGATGGACGAAATGGATGATAAGgtctgttatc ... atgattgtagGTGGATAGAGCCAATGCAGATTTGAAGAATACCAACGTGAGACTGAAGGAG
EST: gi|149015005|gb|EE044748.2|EE044748
EST:     GAATTGGACAGACAAGTCCCTCTGATGGACGAAATGGATGATAAG                         GTGGATAGAGCCAATGCAGATTTGAAGAATACCAACGTGAGACTGAAGGAG
genomic: GAATTGGACAGACAAGTCCCTCTGATGGACGAAATGGATGATAAGgtctgttatc ... atgattgtagGTGGATAGAGCCAATGCAGATTTGAAGAATACCAACGTGAGACTGAAGGAG
EST: gi|5608427|gb|AI902004.1|AI902004
EST:     GAATTGGCCAGCCAAGTCCCTCTGATGGACGAAATGGATGATAAG                         GTGGATAGAGCCAATGCAGATTTGAAGAATACCAACGTGAGACTGAAGGAG
genomic: GAATTGGACAGACAAGTCCCTCTGATGGACGAAATGGATGATAAGgtctgttatc ... atgattgtagGTGGATAGAGCCAATGCAGATTTGAAGAATACCAACGTGAGACTGAAGGAG

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: 45 (upstream exon), 49 (downstream exon)
Score: 363

GAATTGGACAGACAAGTCCCTCTGATGGACGAAATGGATGATAAGgtctgttatc ... atgattgtagGTGGATAGAGCCAATGCAGATTTGAAGAATACCAACGTGAGACTGAAGGAGACTGTTCTTCAA


Block sizes: 45 (upstream exon), 49 (downstream exon)
Score: 449

GAATTGGACAGACAAGTCCCTCTGATGGACGAAATGGATGATAAGgtctgttatc ... atgattgtagGTGGATAGAGCCAATGCAGATTTGAAGAATACCAACGTGAGACTGAAGGAGACTGTTCTTCAA


Block sizes: 45 (upstream exon), 49 (downstream exon)
Score: 376

GAATTGGACAGACAAGTCCCTCTGATGGACGAAATGGATGATAAGgtctgttatc ... atgattgtagGTGGATAGAGCCAATGCAGATTTGAAGAATACCAACGTGAGACTGAAGGAGACTGTTCTTCAA


Block sizes: 45 (upstream exon), 49 (downstream exon)
Score: 335

GAATTGGACAGACAAGTCCCTCTGATGGACGAAATGGATGATAAGgtctgttatc ... atgattgtagGTGGATAGAGCCAATGCAGATTTGAAGAATACCAACGTGAGACTGAAGGAGACTGTTCTTCAA




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tggctcccagaaattgtctagcaactcttattttgctacataatgatgattgtagGTGGATAGAGCCAATGCAGATTTGAAGAATACCAACGTGAGACTGAAGGAGACTGTTCTTCAA
                         tcttatttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtctgttatctggcagccattagttttcgttggctcccagaaattgtctagcaactcttattttgctacataatgatgattgtagGTGGATAGAGCCAATGCAGATTTGAAGAATACCAACGTGAGACTGAAGGAGACTGTTCTTCAA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGGAGA