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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GCACTGGTGGGAGAAGCTGCAAATGATCTTCAGGAGTACTTCAGAACAATGTACAAGAAGgtatgttttcttctatgtcaattgcaggctaatgctgtctattagtttacaatgggctgtttttaggaaaacacagtggggaaaagcctgctgtggcaca...

Basic information

species Zea mays
transcript GRMZM2G129987_T01
intron # 4
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G129987_T01 (Zea mays), 5'ss of exon 4
lower sequence: LOC_Os02g10220.1 (Oryza sativa), 5'ss of exon 4
GCACTGGTGGGAGAAGCTGCAAATGATCTTCAGGAGTACTTCAGAACAATGTACAAGAAGgtatgttttct-tctatgtcaattgcagg-ctaatgctgtctattagttt--acaatgggctgtttttaggaaaaca-cagtggggaaaagcctgctgtggcaca
|||||||| |||||||||||| |  ||||||| |||||||||||| |  | ||||| ||||||| ||||   || || ||||    |   ||  |||| ||| ||    |  ||||||  | ||  | |   | ||  | |  |                     
GCACTGGTTGGAGAAGCTGCAGACAATCTTCAAGAGTACTTCAGAGCTGTTTACAAAAAGgtatctttttggtccatatcaacaaaaaaacttgtgctatctgttcacctatacaatgatcggtgatgacctacacttctgcag---------------------

upper sequence: GRMZM2G129987_T01 (Zea mays), 5'ss of exon 4
lower sequence: GLYMA19G32480.1 (Glycine max), 5'ss of exon 4
GCACTGGTGGGAGAAGCTGCAAATGATCTTCAGGAGTACTTCAGAACAATGTACAAGAAGgtatgttttcttctatgtcaattgcaggctaatgctgtctattagtttacaatgggctgtttttaggaaaacacagtgggga--aaagcctgctgtggcaca
|  || |  ||||| | ||   |  ||||||| |||| ||| |||||||||||||||||||||| | || |  ||| | |  |   |    || |||| |  || |  |   |||  | ||| |    |   |  |||| |   |||   ||||   |    
GACCTTGCTGGAGATGTTGTTCAGAATCTTCAAGAGTTCTTTAGAACAATGTACAAGAAGgtatttgttttaatatatgatatatgg---tattctgttttctaatccattgtggtatatttgtgttcatttat-gtggtgcttaaaatgtgctacag----
















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|78111290|gb|DV529687.1|DV529687
EST:     GAGAAGCTGCAAATGATCTTCAGGAGTACTTCAGAACAATGTACAAGAAG                         GTCACTGAGGCTGACATTGAAGAATTTGAAGCTAAATACAGAGGGTCAGAT
genomic: GAGAAGCTGCAAATGATCTTCAGGAGTACTTCAGAACAATGTACAAGAAGgtatgttttc ... tttgtcccagGTCACTGAGGCTGACATTGAAGAATTTGAAGCTAAATACAGAGGGTCAGAT
EST: gi|31628006|gb|CD526397.1|CD526397
EST:     GAGAAGCTGCAAATGATCTTCAGGAGTACTTCAGAACAATGTACAAGAAG                         GTCACTGAGGCTGACATTGAAGAATTTGAAGCTAAATACAGAGGGTCAGAT
genomic: GAGAAGCTGCAAATGATCTTCAGGAGTACTTCAGAACAATGTACAAGAAGgtatgttttc ... tttgtcccagGTCACTGAGGCTGACATTGAAGAATTTGAAGCTAAATACAGAGGGTCAGAT
EST: gi|31664549|gb|CD573482.1|CD573482
EST:     GAGAAGCTGCAAATGATCTTCAGGAGTACTTCAGAACAATGTACAAGAAG                         GTCACTGAGGCTGACATTGAAGAATTTGAAGCTAAATACAGAGGGTCAGAT
genomic: GAGAAGCTGCAAATGATCTTCAGGAGTACTTCAGAACAATGTACAAGAAGgtatgttttc ... tttgtcccagGTCACTGAGGCTGACATTGAAGAATTTGAAGCTAAATACAGAGGGTCAGAT
EST: gi|19436724|gb|BM953134.1|BM953134
EST:     GAGAAGCTGCAAATGATCTTCAGGAGTACTTCAGAACAATGTACAAGAAG                         GTCACTGAGGCTGACATTGAAGAATTTGAAGCTAAATACAGAGGGTCAGAT
genomic: GAGAAGCTGCAAATGATCTTCAGGAGTACTTCAGAACAATGTACAAGAAGgtatgttttc ... tttgtcccagGTCACTGAGGCTGACATTGAAGAATTTGAAGCTAAATACAGAGGGTCAGAT
EST: gi|149009177|gb|EE041301.2|EE041301
EST:     GAGAAGCTGCAAATGATCTTCAGGAGTACTTCAGAACAATGTACAAGAAG                         GTCACTGAGGCTGACATTGAAGAATTTGAAGCTAAATACAGAGGGTCAGAT
genomic: GAGAAGCTGCAAATGATCTTCAGGAGTACTTCAGAACAATGTACAAGAAGgtatgttttc ... tttgtcccagGTCACTGAGGCTGACATTGAAGAATTTGAAGCTAAATACAGAGGGTCAGAT
EST: gi|91053239|gb|EB163657.1|EB163657
EST:     GAGAAGCTGCAAATGATCTTCAGGAGTACTTCAGAACAATGTACAAGAAG                         GTCACTGAGGCTGACATTGAAGAATTTGAAGCTAAATACAGAGGGTCAGAT
genomic: GAGAAGCTGCAAATGATCTTCAGGAGTACTTCAGAACAATGTACAAGAAGgtatgttttc ... tttgtcccagGTCACTGAGGCTGACATTGAAGAATTTGAAGCTAAATACAGAGGGTCAGAT
EST: gi|76011893|gb|DT939063.1|DT939063
EST:     GAGAAGCTGCAAATGATCTTCAGGAGTACTTCAGAACAATGTACAAGAAG                         GTCACTGAGGCTGACATTGAAGAATTTGAAGCTAAATACAGAGGGTCAGAT
genomic: GAGAAGCTGCAAATGATCTTCAGGAGTACTTCAGAACAATGTACAAGAAGgtatgttttc ... tttgtcccagGTCACTGAGGCTGACATTGAAGAATTTGAAGCTAAATACAGAGGGTCAGAT
EST: gi|71771230|gb|DR969167.1|DR969167
EST:     GAGAAGCTGCAAATGATCTTCAGGAGTACTTCAGAACAATGTACAAGAAG                         GTCACTGAGGCTGACATTGAAGAATTTGAAGCTAAATACAGAGGGTCAGAT
genomic: GAGAAGCTGCAAATGATCTTCAGGAGTACTTCAGAACAATGTACAAGAAGgtatgttttc ... tttgtcccagGTCACTGAGGCTGACATTGAAGAATTTGAAGCTAAATACAGAGGGTCAGAT
EST: gi|78082398|gb|DV510810.1|DV510810
EST:     GAGAAGCTGCAAATGATCTTCAGGAGTACTTCAGAACAATGTACAAGAAG                         GTCACTGAGGCTGACATTGAAGAATTTGAAGCTAAATACAGAGGGTCAGAT
genomic: GAGAAGCTGCAAATGATCTTCAGGAGTACTTCAGAACAATGTACAAGAAGgtatgttttc ... tttgtcccagGTCACTGAGGCTGACATTGAAGAATTTGAAGCTAAATACAGAGGGTCAGAT
EST: gi|211448244|gb|FK956529.1|FK956529
EST:     GAGAAGCTGCAAATGATCTTCAGGAGTACTTCAGAACAATGTACAAGAAG                         GTCACTGAGGCTGACATTGAAGAATTTGAAGCTAAATACAGAGGG
genomic: GAGAAGCTGCAAATGATCTTCAGGAGTACTTCAGAACAATGTACAAGAAGgtatgttttc ... tttgtcccagGTCACTGAGGCTGACATTGAAGAATTTGAAGCTAAATACAGAGGG
EST: gi|19057616|gb|BM736283.1|BM736283
EST:     GAGAAGCTGCAAATGATCTTCAGGAGTACTTCAGAACAATGTACAAGAAG                         GTCACTGAGGCTGACATTGAAGAATTTGAAGCTAAATACAGAGGGTCAGAT
genomic: GAGAAGCTGCAAATGATCTTCAGGAGTACTTCAGAACAATGTACAAGAAGgtatgttttc ... tttgtcccagGTCACTGAGGCTGACATTGAAGAATTTGAAGCTAAATACAGAGGGTCAGAT
EST: gi|19436292|gb|BM952702.1|BM952702
EST:     GAGAAGCTGCAAATGATCTTCAGGAGTACTTCAGAACAATGTACAAGAAG                         GTCACTGAGGCTGACATTGAAGAATTTGAAGCTAAATACAGAGGGTCAGAT
genomic: GAGAAGCTGCAAATGATCTTCAGGAGTACTTCAGAACAATGTACAAGAAGgtatgttttc ... tttgtcccagGTCACTGAGGCTGACATTGAAGAATTTGAAGCTAAATACAGAGGGTCAGAT
EST: gi|71320398|gb|DR796949.1|DR796949
EST:     GAGAAGCTGCAAATGATCTTCAGGAGTACTTCAGAACAATGTACAAGAAG                         GTCACTGAGGCTGACATTGAAGAATTTGAAGCTAAATACAGAGGGTCAGAT
genomic: GAGAAGCTGCAAATGATCTTCAGGAGTACTTCAGAACAATGTACAAGAAGgtatgttttc ... tttgtcccagGTCACTGAGGCTGACATTGAAGAATTTGAAGCTAAATACAGAGGGTCAGAT
EST: gi|211448242|gb|FK956527.1|FK956527
EST:     GAGAAGCTGCAAATGATCTTCAGGAGTACTTCAGAACAATGTACAAGAAG                         GTCACTGAGGCTGACATTGAAGAATTTGAAGCTAAATACAGAG
genomic: GAGAAGCTGCAAATGATCTTCAGGAGTACTTCAGAACAATGTACAAGAAGgtatgttttc ... tttgtcccagGTCACTGAGGCTGACATTGAAGAATTTGAAGCTAAATACAGAG
EST: gi|211450351|gb|FK956532.1|FK956532
EST:     GAGAAGCTGCAAATGATCTTCAGGAGTACTTCAGAACAATGTACAAGAAG                         GTCACTGAGGCTGACATTGAAGAATTTGAAGCTAAATACAGAGGGTCAGAT
genomic: GAGAAGCTGCAAATGATCTTCAGGAGTACTTCAGAACAATGTACAAGAAGgtatgttttc ... tttgtcccagGTCACTGAGGCTGACATTGAAGAATTTGAAGCTAAATACAGAGGGTCAGAT
EST: gi|19436725|gb|BM953135.1|BM953135
EST:     GAGAAGCTGCAAATGATCTTCAGGAGTACTTCAGAACAATGTACAAGAAG                         GTCACTGAGGCTGACATTGAAGAATTGGAAGCTAAATACAGAGGGTCAGAT
genomic: GAGAAGCTGCAAATGATCTTCAGGAGTACTTCAGAACAATGTACAAGAAGgtatgttttc ... tttgtcccagGTCACTGAGGCTGACATTGAAGAATTTGAAGCTAAATACAGAGGGTCAGAT
EST: gi|91054843|gb|EB165261.1|EB165261
EST:     GAGAAGCTGCAAATGATCTTCAGGAGTACTTCAGAACAATGTACAAGAAG                         GTCACTGAGGCTGACATTGAAGAATTTGAAGCTAAATACAGAGGGTCAGAT
genomic: GAGAAGCTGCAAATGATCTTCAGGAGTACTTCAGAACAATGTACAAGAAGgtatgttttc ... tttgtcccagGTCACTGAGGCTGACATTGAAGAATTTGAAGCTAAATACAGAGGGTCAGAT
EST: gi|211448245|gb|FK956530.1|FK956530
EST:     GAGAAGCTGCAAATGATCTTCAGGAGTACTTCAGAACAATGTACAAGAAG                         GTCACTGAGGCTGACATTGAAGA
genomic: GAGAAGCTGCAAATGATCTTCAGGAGTACTTCAGAACAATGTACAAGAAGgtatgttttc ... tttgtcccagGTCACTGAGGCTGACATTGAAGA
EST: gi|76924244|gb|DV169873.1|DV169873
EST:     GAGAAGCTGCAAATGATCTTCAGGAGTACTTCAGAACAATGTACAAGAAG                         GTCACTGAGGCTGACATTGAAGAATTTGAAGCTAAATACAGAGGGTCAGAT
genomic: GAGAAGCTGCAAATGATCTTCAGGAGTACTTCAGAACAATGTACAAGAAGgtatgttttc ... tttgtcccagGTCACTGAGGCTGACATTGAAGAATTTGAAGCTAAATACAGAGGGTCAGAT
EST: gi|71315532|gb|DR794370.1|DR794370
EST:     AGAAGCTGCAAATGATCTTCAGGAGTACTTCAGAAACA-TGTACAAGAAG                         GTCACTGAGGCTGACA
genomic: AGAAGCTGCAAATGATCTTCAGGAGTACTTCAGAA-CAATGTACAAGAAGgtatgttttc ... tttgtcccagGTCACTGAGGCTGACA

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: 343

GCACTGGTGGGAGAAGCTGCAAATGATCTTCAGGAGTACTTCAGAACAATGTACAAGAAGgtatgttttc ... tttgtcccagGTCACTGAGGCTGACATTGAAGAATTTGAAGCTAAATACAGAGGGTCAGATTCTGAGAAAACGGACTTGAAGGAACTCTACACAAAATATAAGGGCAACA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 74

GCACTGGTGGGAGAAGCTGCAAATGATCTTCAGGAGTACTTCAGAACAATGTACAAGAAGgtatgttttc ... tttgtcccagGTCACTGAGGCTGACATTGAAGAATTTGAAGCTAAATACAGAGGGTCAGATTCTGAGAAAACGGACTTGAAGGAACTCTACACAAAATATAAGGGCAACA


Block sizes: 46 (upstream exon), 49 (downstream exon)
Score: 84

GCACTGGTGGGAGAAGCTGCAAATGATCTTCAGGAGTACTTCAGAACAATGTACAAGAAGgtatgttttc ... tttgtcccagGTCACTGAGGCTGACATTGAAGAATTTGAAGCTAAATACAGAGGGTCAGATTCTGAGAAAACGGACTTGAAGGAACTCTACACAAAATATAAGGGCAACA


Block sizes: 49 (upstream exon), 44 (downstream exon)
Score: 43

GCACTGGTGGGAGAAGCTGCAAATGATCTTCAGGAGTACTTCAGAACAATGTACAAGAAGgtatgttttc ... tttgtcccagGTCACTGAGGCTGACATTGAAGAATTTGAAGCTAAATACAGAGGGTCAGATTCTGAGAAAACGGACTTGAAGGAACTCTACACAAAATATAAGGGCAACA


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GCACTGGTGGGAGAAGCTGCAAATGATCTTCAGGAGTACTTCAGAACAATGTACAAGAAGgtatgttttcttctatgtcaattgcaggctaatgctgtctattagtttacaatgggctgtttttaggaaaacacagtggggaaaagcctgctgtggcaca

- - - - -  AGAAGC
- - - - - -  AAGCTG
- - - - - - - AGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -aaaacaca