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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GCTTGGGTAGTGGAAGGCGTCGCAGCCGAAGTCCTAGATATCGCAGCCGCAGCCGCAGCCGCAGCCCAAGATATCGAAGGAGCCCAAGCTATAGCAGAAGgtaatttgctaatgacaccaattcaccacatgtattcatccagtagttttaattaagggttgggaaacacgacctagaaatcctaaaacttttgagaacg...

Basic information

species Zea mays
transcript GRMZM2G027105_T04
intron # 4
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G027105_T04 (Zea mays), 5'ss of exon 4
lower sequence: LOC_Os02g39720.4 (Oryza sativa), 5'ss of exon 4
GCTTGGGTAGTGGAAGGCGTCGCAGCCGAAGTCCTAGATATCGCAGCCGCAGCCGCAGCCGCAGCCCAAGATATCGAAGGAGCCCAAGCTATAGCAGAAGgtaatttgctaatgacaccaattcaccacatgtattcatccagtagttttaattaagggttgggaaacacgacctagaaatcctaaaacttttgagaacg-----------
|     |  |  |  |  | || ||||| ||||| || || ||| | || || |||||||||||||||||||| || ||||||||||||||| | |||||||||| |   || |  |     |    ||| |   |      |||| | | | ||| |        | |   | | | |  |||| |   |||      |           
GAAGACGCCGCAGCCGCAGCCGTAGCCGGAGTCCAAGGTACCGCGGTCGTAGTCGCAGCCGCAGCCCAAGATACCGGAGGAGCCCAAGCTATGGTAGAAGgtaatgt---aaagttattgtcttcaaacaggctct------gtagatatgagtaatgacaaaatgatat--cttggcatccctagattctttcttgttggccagccaaat
















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|15188227|gb|BI417204.1|BI417204
EST:     AGCCGCAGCCGCAGCCCAAGATATCGAAGGAGCCCAAGCTATAGCAGAAG                         CCCGCGAGATCGTTCTCCTAGGAGGCGAAGTTACAGCAGGTCGCCACTGGG
genomic: AGCCGCAGCC-CA----A-GATATCGAAGGAGCCCAAGCTATAGCAGAAGgtaatttgct ... ggagctacagCCCGCGAGATCGTTCTCCTAGGAGGCGAAGTTACAGCAGGTCGCCACTGGG
EST: gi|60350338|gb|DN217311.1|DN217311
EST:     AGCCGCAGCCGCAGCCCAAGATATCGAAGGAGCCCAAGCTATAGCAGAAG                         CCCGCGAGATCGTTCTCCTAGGAGGCGAAGTTACAGCAGGTCGCCACTGGG
genomic: AGCCGCAGCCGCAGCCCAAGATATCGAAGGAGCCCAAGCTATAGCAGAAGgtaatttgct ... ggagctacagCCCGCGAGATCGTTCTCCTAGGAGGCGAAGTTACAGCAGGTCGCCACTGGG
EST: gi|71759159|gb|DR957096.1|DR957096
EST:     AAGCTATAGCAGAAG                         CCCGCGAGATCGTTCTCCTAGGAGGCGAAGTTACAGCAGGTCGCCACTGGG
genomic: AAGCTATAGCAGAAGgtaatttgct ... ggagctacagCCCGCGAGATCGTTCTCCTAGGAGGCGAAGTTACAGCAGGTCGCCACTGGG
EST: gi|20337024|gb|BQ172654.1|BQ172654
EST:     GCTATAGCAGAAG                         CCCGCGAGGTCGTTCTCCTAGGAGGCGAAGTTACAGCAGGTCGCCACTGGG
genomic: GCTATAGCAGAAGgtaatttgct ... ggagctacagCCCGCGAGATCGTTCTCCTAGGAGGCGAAGTTACAGCAGGTCGCCACTGGG
EST: gi|21331667|gb|BQ487048.1|BQ487048
EST:     AGCCGCAGCCGCAGCCCAAGATATCGAAGGAGCCCAAGCTATAGCAGAAG                         CCCGCGAGGTCGTTCTCCTAGGAGGCGAAGTTACAGCAGGTCGCCACTGGG
genomic: AGCCGCAGCCGCAGCCCAAGATATCGAAGGAGCCCAAGCTATAGCAGAAGgtaatttgct ... ggagctacagCCCGCGAGATCGTTCTCCTAGGAGGCGAAGTTACAGCAGGTCGCCACTGGG
EST: gi|148953639|gb|EC898996.2|EC898996
EST:     AGCCCAAGATATCGAAGGAGCCCAAGCTATAGCAGAAG                         CCCGCGAGATCGTTCTCCTAGGAGGCGAAGTTACAGCAGGTCGCCACTGGG
genomic: AGCCCAAGATATCGAAGGAGCCCAAGCTATAGCAGAAGgtaatttgct ... ggagctacagCCCGCGAGATCGTTCTCCTAGGAGGCGAAGTTACAGCAGGTCGCCACTGGG
EST: gi|22489522|gb|BU049445.1|BU049445
EST:     AGCCGCAGCCGCAGCCCAAGATATCGAAGGAGCCCAAGCTATAGCAGAAG                         CCCGCGAGATCGTTCTCCTAGGAGGCGAAGTTACAGCAGGTCGCCACTGGG
genomic: AGCCGCAGCC-CA----A-GATATCGAAGGAGCCCAAGCTATAGCAGAAGgtaatttgct ... ggagctacagCCCGCGAGATCGTTCTCCTAGGAGGCGAAGTTACAGCAGGTCGCCACTGGG
EST: gi|18384821|gb|BM418020.1|BM418020
EST:     AGCCGCAGCCGCAGCCCAAGATATCGAAGGAGCCCAAGCTATAGCAGAAG                         CCCGCGAGATCGTTCTCCTAGGAGGCGAAGTTACAGCAGGTCGCCACTGGG
genomic: AGCCGCAGCC-CA----A-GATATCGAAGGAGCCCAAGCTATAGCAGAAGgtaatttgct ... ggagctacagCCCGCGAGATCGTTCTCCTAGGAGGCGAAGTTACAGCAGGTCGCCACTGGG
EST: gi|71438201|gb|DR819251.1|DR819251
EST:     AGCCGCAGCCGCAGCCCAAGATATCGAAGGAGCCCAAGCTATAGCAGAAG                         CCCGCGAGATCGTTCTCCTAGGAGGCGAAGTTACAGCAGGTCGCCACTGGG
genomic: AGCCGCAGCCGCAGCCCAAGATATCGAAGGAGCCCAAGCTATAGCAGAAGgtaatttgct ... ggagctacagCCCGCGAGATCGTTCTCCTAGGAGGCGAAGTTACAGCAGGTCGCCACTGGG
EST: gi|22489415|gb|BU049338.1|BU049338
EST:     AGCCGCAGCCGCAGCCCAAGATATCGAAGGAGCCCAAGCTATAGCAGAAG                         CCCGCGAGATCGTTCTCCTAGGAGGCGAAGTTACAGCAGGTCGCCACTGGG
genomic: AGCCGCAGCC-CA----A-GATATCGAAGGAGCCCAAGCTATAGCAGAAGgtaatttgct ... ggagctacagCCCGCGAGATCGTTCTCCTAGGAGGCGAAGTTACAGCAGGTCGCCACTGGG
EST: gi|15177619|gb|BI398558.1|BI398558
EST:     AGCCGCAGCCGCAGCCCAAGATATCGAAGGAGCCCAAGCTATAGCAGAAG                         CCCGCGAGATCGTTCTCCTAGGAGGCGA
genomic: AGCCGCAGCC-CA----A-GATATCGAAGGAGCCCAAGCTATAGCAGAAGgtaatttgct ... ggagctacagCCCGCGAGATCGTTCTCCTAGGAGGCGA
EST: gi|88758547|gb|DY542916.1|DY542916
EST:     AGCCGCAGCCGCAGCCCAAGATATCGAAGGAGCCCAAGCTATAGCAGAAG                         CCCGCGAGATCGTTCTCCTAGGAGGCGAAGTTACAGCAGGTCGCCACTGGG
genomic: AGCCGCAGCC-CA----A-GATATCGAAGGAGCCCAAGCTATAGCAGAAGgtaatttgct ... ggagctacagCCCGCGAGATCGTTCTCCTAGGAGGCGAAGTTACAGCAGGTCGCCACTGGG
EST: gi|18053132|gb|BM318790.1|BM318790
EST:     AGCCGCAGCCGCAGCCCAAGATATCGAAGGAGCCCAAGCTATAGCAGAAG                         CCCGCGAGATCGTTCTCCTAGGAGGCGAAGTTACAGCAGGTCGCCACTGGG
genomic: AGCCGCAGCC-CA----A-GATATCGAAGGAGCCCAAGCTATAGCAGAAGgtaatttgct ... ggagctacagCCCGCGAGATCGTTCTCCTAGGAGGCGAAGTTACAGCAGGTCGCCACTGGG
EST: gi|26456505|gb|CA828088.1|CA828088
EST:     AGCCGCAGCCGCAGCCCAAGATATCGAAGGAGCCCAAGCTATAGCAGAAG                         CCCGCGAGGTCGTTCTCCTAGGAGGCGAAGTTACAGCAGGTCGCCACTGGG
genomic: AGCCGCAGCCGCAGCCCAAGATATCGAAGGAGCCCAAGCTATAGCAGAAGgtaatttgct ... ggagctacagCCCGCGAGATCGTTCTCCTAGGAGGCGAAGTTACAGCAGGTCGCCACTGGG
EST: gi|20803218|gb|BQ294268.1|BQ294268
EST:     AGCCGCAGCCGCAGCCCAAGATATCGAAGGAGCCCAAGCTATAGCAGAAG                         CCCGCGAGGTCGTTCTCCTAGGAGGCGAAGTTACAGCAGGTCGCCACTGGG
genomic: AGCCGCAGCCGCAGCCCAAGATATCGAAGGAGCCCAAGCTATAGCAGAAGgtaatttgct ... ggagctacagCCCGCGAGATCGTTCTCCTAGGAGGCGAAGTTACAGCAGGTCGCCACTGGG
EST: gi|18178383|gb|BM379593.1|BM379593
EST:     GCCGCAGCCCAAGATATCGAAGGAGCCCAAGCTATAGCAGAAG                         CCCGCGAGATCGTTCTCCTAGGAGGCGAAGTTACAGCAGGTCGCCACTGGG
genomic: GCCGCAGCCCAAGATATCGAAGGAGCCCAAGCTATAGCAGAAGgtaatttgct ... ggagctacagCCCGCGAGATCGTTCTCCTAGGAGGCGAAGTTACAGCAGGTCGCCACTGGG
EST: gi|71449212|gb|DR830262.1|DR830262
EST:     AGCCGCAGCCGCAGCCCAAGATATCGAAGGAGCCCAAGCTATAGCAGAAG                         CCCGCGAGATCGTTCTCCTAGGAGGCGAAGTTACAGCAGGTCGCCACTGGG
genomic: AGCCGCAGCCGCAGCCCAAGATATCGAAGGAGCCCAAGCTATAGCAGAAGgtaatttgct ... ggagctacagCCCGCGAGATCGTTCTCCTAGGAGGCGAAGTTACAGCAGGTCGCCACTGGG
EST: gi|17970002|gb|BM276770.1|BM276770
EST:     AGCCGCAGCCGCAGCCCAAGATATCGAAGGAGCCCAAGCTATAGCAGAAG                         CCCGCGAGATCGTTCTCCTAGGAGGCGAAGTTACAGCAGGTCGCCACTGGG
genomic: AGCCGCAGCC-CA----A-GATATCGAAGGAGCCCAAGCTATAGCAGAAGgtaatttgct ... ggagctacagCCCGCGAGATCGTTCTCCTAGGAGGCGAAGTTACAGCAGGTCGCCACTGGG
EST: gi|18384819|gb|BM418018.1|BM418018
EST:     AGCCGCAGCCGCAGCCCAAGATATCGAAGGAGCCCAAGCTATAGCAGAAG                         CCCGCGAGATC
genomic: AGCCGCAGCC-CA----A-GATATCGAAGGAGCCCAAGCTATAGCAGAAGgtaatttgct ... ggagctacagCCCGCGAGATC
EST: gi|87298765|gb|DY470768.1|DY470768
EST:     AGCCGCAGCCGCAGCCCAAGATATCGAAGGAGCCCAAGCTATAGCAGAAG                         CCCGCGAGATCGTTCTCCTAGGAGGCGAAGTTACAGCAGGTCGCCACTGGG
genomic: AGCCGCAGCC-CA----A-GATATCGAAGGAGCCCAAGCTATAGCAGAAGgtaatttgct ... ggagctacagCCCGCGAGATCGTTCTCCTAGGAGGCGAAGTTACAGCAGGTCGCCACTGGG
EST: gi|18053144|gb|BM318802.1|BM318802
EST:     AGCCGCAGCCGCAGCCCAAGATATCGAAGGAGCCCAAGCTATAGCAGAAG                         CCCGCGAGATCGTTCTCCTAGGAGGCGAAGTTACAGCAGGTCGCCACTGGG
genomic: AGCCGCAGCC-CA----A-GATATCGAAGGAGCCCAAGCTATAGCAGAAGgtaatttgct ... ggagctacagCCCGCGAGATCGTTCTCCTAGGAGGCGAAGTTACAGCAGGTCGCCACTGGG
EST: gi|71317875|gb|DR795704.1|DR795704
EST:     AGCCGCAGCCGCAGCCCAAGATATCGAAGGAGCCCAAGCTATAGCAGAAG                         CCCGCGAGATCGTTCTCCTAGGAGGCGAAGTTACAGCAGGTCGCCACTGGG
genomic: AGCCGCAGCCGCAGCCCAAGATATCGAAGGAGCCCAAGCTATAGCAGAAGgtaatttgct ... ggagctacagCCCGCGAGATCGTTCTCCTAGGAGGCGAAGTTACAGCAGGTCGCCACTGGG
EST: gi|71758988|gb|DR956925.1|DR956925
EST:     CAAGCTATAGCAGAAG                         CCCGCGAGATGGTTCTCCTAGGAGGCGAAGTTACAGCAGGTCGCCACTGGG
genomic: CAAGCTATAGCAGAAGgtaatttgct ... ggagctacagCCCGCGAGATCGTTCTCCTAGGAGGCGAAGTTACAGCAGGTCGCCACTGGG
EST: gi|18384989|gb|BM418188.1|BM418188
EST:     AGCCGCAGCCGCAGCCCAAGATATCGAAGGAGCCCAAGCTATAGCAGAAG                         CCCGCGAGATCGTTCTCCTAGGAGGCGAAGTTACAGCAGGTCGCCACTGGG
genomic: AGCCGCAGCC-CA----A-GATATCGAAGGAGCCCAAGCTATAGCAGAAGgtaatttgct ... ggagctacagCCCGCGAGATCGTTCTCCTAGGAGGCGAAGTTACAGCAGGTCGCCACTGGG
EST: gi|15188220|gb|BI417197.1|BI417197
EST:     AGCCGCAGCCGCAGCCCAAGATATCGAAGGAGCCCAAGCTATAGCAGAAG                         CCCGCGAGATCGTTCTCCTAGGAGGGCGAAGTTACAGCAGGTCGCCACTGG
genomic: AGCCGCAGCC-CA----A-GATATCGAAGGAGCCCAAGCTATAGCAGAAGgtaatttgct ... ggagctacagCCCGCGAGATCGTTCTCCTAGGAGG-CGAAGTTACAGCAGGTCGCCACTGG
EST: gi|50333998|gb|CO529124.1|CO529124
EST:     AGCCGCAGCCGCAGCCCAAGATATCGAAGGAGCCCAAGCTATAGCAGAAG                         CCCGCGAGATCGTTCTCCTAGGAGGCGAAGTTACAGCAGGTCGCCACTGGG
genomic: AGCCGCAGCCGCAGCCCAAGATATCGAAGGAGCCCAAGCTATAGCAGAAGgtaatttgct ... ggagctacagCCCGCGAGATCGTTCTCCTAGGAGGCGAAGTTACAGCAGGTCGCCACTGGG
EST: gi|18384820|gb|BM418019.1|BM418019
EST:     AGCCGCAGCCGCAGCCCAAGATATCGAAGGAGCCCAAGCTATAGCAGAAG                         CCCGCGAGATCGTTCTCCTAGGAGGCGAAGTTACAGCAGGTCGCCACTGGG
genomic: AGCCGCAGCC-CA----A-GATATCGAAGGAGCCCAAGCTATAGCAGAAGgtaatttgct ... ggagctacagCCCGCGAGATCGTTCTCCTAGGAGGCGAAGTTACAGCAGGTCGCCACTGGG
EST: gi|50338081|gb|CO533207.1|CO533207
EST:     AGCCGCAGCCGCAGCCCAAGATATCGAAGGAGCCCAAGCTATAGCAGAAG                         CCCGCGAGATCGTTCTCCTAGGAGGCGAAGTTACAGCAGGTCGCCACTGGG
genomic: AGCCGCAGCCGCAGCCCAAGATATCGAAGGAGCCCAAGCTATAGCAGAAGgtaatttgct ... ggagctacagCCCGCGAGATCGTTCTCCTAGGAGGCGAAGTTACAGCAGGTCGCCACTGGG
EST: gi|71317873|gb|DR795703.1|DR795703
EST:     CTATAGCAGAAG                         CCCGCGAGATCGTTCTCCTAGGAGGGGAAGTTACAGCAGGTCGCCACTGGG
genomic: CTATAGCAGAAGgtaatttgct ... ggagctacagCCCGCGAGATCGTTCTCCTAGGAGGCGAAGTTACAGCAGGTCGCCACTGGG
EST: gi|22489184|gb|BU049107.1|BU049107
EST:     AGCCGCAGCCGCAGCCCAAGATATCGAAGGAGCCCAAGCTATAGCAGAAG                         CCCGCGAGATCGTTCTCCTAGGAGGCGAAGTTACAGCAGGTCGCCACTGGG
genomic: AGCCGCAGCC-CA----A-GATATCGAAGGAGCCCAAGCTATAGCAGAAGgtaatttgct ... ggagctacagCCCGCGAGATCGTTCTCCTAGGAGGCGAAGTTACAGCAGGTCGCCACTGGG
EST: gi|71438000|gb|DR819050.1|DR819050
EST:     AGCCGCAGCCGCAGCCCAAGATATCGAAGGAGCCCAAGCTATAGCAGAAG                         CCCGCGAGATCGTTCTCCTAGGAGGCGAAGTTACAGCAGGTCGCCACTGGG
genomic: AGCCGCAGCCGCAGCCCAAGATATCGAAGGAGCCCAAGCTATAGCAGAAGgtaatttgct ... ggagctacagCCCGCGAGATCGTTCTCCTAGGAGGCGAAGTTACAGCAGGTCGCCACTGGG
EST: gi|18383855|gb|BM417055.1|BM417055
EST:     AGCCGCAGCCGCAGCCCAAGATATCGAAGGAGCCCAAGCTATAGCAGAAG                         CCCGCGAGATCGTTCTCCTAGGAGGCGAAGTTACAGCAGGTCGCCACTGGG
genomic: AGCCGCAGCC-CA----A-GATATCGAAGGAGCCCAAGCTATAGCAGAAGgtaatttgct ... ggagctacagCCCGCGAGATCGTTCTCCTAGGAGGCGAAGTTACAGCAGGTCGCCACTGGG

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: 21 (upstream exon), 48 (downstream exon)
Score: 15

GCTTGGGTAGTGGAAGGCGTCGCAGCCGAAGTCCTAGATATCGCAGCCGCAGCCGCAGCCGCAGCCCAAGATATCGAAGGAGCCCAAGCTATAGCAGAAGgtaatttgct ... ggagctacagCCCGCGAGATCGTTCTCCTAGGAGGCGAAGTTACAGCAGGTCGCCACTGGGATCTCCTGCACGGAGTCTCAGCAGGTCACCGCCGCTGCCGCCGCCTCCT


Block sizes: 44 (upstream exon), 47 (downstream exon)
Score: 17

GCTTGGGTAGTGGAAGGCGTCGCAGCCGAAGTCCTAGATATCGCAGCCGCAGCCGCAGCCGCAGCCCAAGATATCGAAGGAGCCCAAGCTATAGCAGAAGgtaatttgct ... ggagctacagCCCGCGAGATCGTTCTCCTAGGAGGCGAAGTTACAGCAGGTCGCCACTGGGATCTCCTGCACGGAGTCTCAGCAGGTCACCGCCGCTGCCGCCGCCTCCT


Block sizes: 45 (upstream exon), 49 (downstream exon)
Score: 10

GCTTGGGTAGTGGAAGGCGTCGCAGCCGAAGTCCTAGATATCGCAGCCGCAGCCGCAGCCGCAGCCCAAGATATCGAAGGAGCCCAAGCTATAGCAGAAGgtaatttgct ... ggagctacagCCCGCGAGATCGTTCTCCTAGGAGGCGAAGTTACAGCAGGTCGCCACTGGGATCTCCTGCACGGAGTCTCAGCAGGTCACCGCCGCTGCCGCCGCCTCCT


Block sizes: 44 (upstream exon), 49 (downstream exon)
Score: 21

GCTTGGGTAGTGGAAGGCGTCGCAGCCGAAGTCCTAGATATCGCAGCCGCAGCCGCAGCCGCAGCCCAAGATATCGAAGGAGCCCAAGCTATAGCAGAAGgtaatttgct ... ggagctacagCCCGCGAGATCGTTCTCCTAGGAGGCGAAGTTACAGCAGGTCGCCACTGGGATCTCCTGCACGGAGTCTCAGCAGGTCACCGCCGCTGCCGCCGCCTCCT


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GCTTGGGTAGTGGAAGGCGTCGCAGCCGAAGTCCTAGATATCGCAGCCGCAGCCGCAGCCGCAGCCCAAGATATCGAAGGAGCCCAAGCTATAGCAGAAGgtaatttgctaatgacaccaattcaccacatgtattcatccagtagttttaattaagggttgggaaacacgacctagaaatcctaaaacttttgagaacg

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAAGCT