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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgagtatttgttccgctctccatttataatcaaatgtttagtttataatctaaatatgcgtcctcattttgttatgcttaaacaattgaaccagGAGTGGAGAATGGGGTGACCACGTTACATTGCAGGCTGCTGCAGACTCG

Basic information

species Zea mays
transcript GRMZM2G035150_T02
intron # 7
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G035150_T02 (Zea mays), 3'ss of exon 7
lower sequence: LOC_Os03g64219.3 (Oryza sativa), 3'ss of exon 6
gtgagtatttgttccgctctccatttataatcaaatgtttagtttataatctaa--atatgcgtcctcattttgttatgcttaaacaattgaaccagGAGTGGAGAATGGGGTGACCACGTTACATTGCAGGCTGCTGCAGACTCG---------------------------------------------------
|| ||||||| |     | |  ||| | ||  |||| |||  |||||| | |||   || || |  ||| |||||   |   | | ||| || ||||||  || || |||||||||||||||||||||||||||||||||||||||                                                   
gtaagtatttctcg---tttttattaacaagtaaatctttgctttatagtgtaacattaggcattttcactttgt---ggccacaaaatcga-ccagGAACGGGGAGTGGGGTGACCACGTTACATTGCAGGCTGCTGCAGACTCGGTAAAGATGATGTTTCCACACTTCCTGACTTATTAAATAATTATTCTTCTG

upper sequence: GRMZM2G035150_T02 (Zea mays), 3'ss of exon 7
lower sequence: LOC_Os03g64219.1 (Oryza sativa), 3'ss of exon 6
gtgagtatttgttccgctctccatttataatcaaatgtttagtttataatctaa--atatgcgtcctcattttgttatgcttaaacaattgaaccagGAGTGGAGAATGGGGTGACCACGTTACATTGCAGGCTGCTGCAGACTCG
|| ||||||| |     | |  ||| | ||  |||| |||  |||||| | |||   || || |  ||| |||||   |   | | ||| || ||||||  || || |||||||||||||||||||||||||||||||||||||||
gtaagtatttctcg---tttttattaacaagtaaatctttgctttatagtgtaacattaggcattttcactttgt---ggccacaaaatcga-ccagGAACGGGGAGTGGGGTGACCACGTTACATTGCAGGCTGCTGCAGACTCG

upper sequence: GRMZM2G035150_T02 (Zea mays), 3'ss of exon 7
lower sequence: GLYMA10G35300.3 (Glycine max), 3'ss of exon 7
----gtgagtattt---gttccgctct-ccatttataatcaaatg--tttagtttataatctaaatatgcgtcctcattttgttatgcttaaacaattgaaccagGAGTGGAGAATGGGGTGACCACGTTACATTGCAGGCTGCTGCAGACTCG
    |||  ||| |    ||  ||| |   |||| | ||||  ||  |||| |||||   ||   | | |      |  || || ||   |      || ||||| ||||| ||||||||||| || || |||||||||||||||||||| | |
gtatgtgcatatctctcattatgctatgttatttctcatcatgtggctttattttatgtcctttgtgttcactgctagctttttgtgtgga------tgtaccagAAGTGGCGAATGGGGTGATCATGTCACATTGCAGGCTGCTGCAGATTGG

upper sequence: GRMZM2G035150_T02 (Zea mays), 3'ss of exon 7
lower sequence: GLYMA20G32220.1 (Glycine max), 3'ss of exon 7
--gtgagtatttgttccgctct-ccat-ttataatcaaatgtttagtttataatctaaatatgcgtcctcattttgttatgcttaaacaattgaaccagGAGTGGAGAATGGGGTGACCACGTTACATTGCAGGCTGCTGCAGACTCG
   || | |  | |  |  | | | || ||||     |   | | || | || | ||    |  ||  ||| |      |  ||       || ||||||||||| ||||||||||| || || || ||||||||||||||||| | |
gtatgtgcacatctctcattatgctatgttatttctgatcatgtggtgt-tattgtagtcctttgtgttcactgatagctttttgtgtggatgtaccagGAGTGGCGAATGGGGTGATCATGTCACGTTGCAGGCTGCTGCAGATTGG

upper sequence: GRMZM2G035150_T02 (Zea mays), 3'ss of exon 7
lower sequence: AT5G04250.2 (Arabidopsis thaliana), 3'ss of exon 7
-gtgagtatttgttccgctctccatttataatcaaatgtttagt-ttataatctaaatatgcgtcctcattttgttatgcttaaacaattgaaccagGAGTGGAGAATGGGGTGACCACGTTACATTGCAGGCTGCTGCAGACTCG
  |    | ||  | | |||     |||  ||   | ||||| | || ||   | |  |    |  | |  || || |  | |        |  ||||| ||||||||||||||| ||||||||  | ||||||||||| || | |
gttcgaaacttaattctctcaattcttaccattgga-gtttactgttttagcttcatcactaatggtgagatttttgtaat-attttgggaagacagGAATGGAGAATGGGGTGATCACGTTACTCTTCAGGCTGCTGCGGATTTG

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|74235678|gb|DT643592.1|DT643592
EST:     GCAGGATATGTCCCTATGGACTACAGGGAATATCTCAAAAAGATGTCAAA                         GAGTGGAGAATGGGGTGACCACGTTACATTGCAGGCTGCTGCAGACTCG
genomic: GCAGGATATGTCCCTATGGACTACAGGGAATATCTCAAAAAGATGTCAAAgtgagtattt ... attgaaccagGAGTGGAGAATGGGGTGACCACGTTACATTGCAGGCTGCTGCAGACTCG
EST: gi|78092883|gb|DV521257.1|DV521257
EST:     GCAGGATATGTCCCTATGGACTACAGGGAATATTTCAAAAAGATGTCAAA                         GAGTGGAGAATGGGGTGACCACGTTACATTGCAGGCTGCTGCAGACTCG
genomic: GCAGGATATGTCCCTATGGACTACAGGGAATATCTCAAAAAGATGTCAAAgtgagtattt ... attgaaccagGAGTGGAGAATGGGGTGACCACGTTACATTGCAGGCTGCTGCAGACTCG
EST: gi|76289426|gb|DV028994.1|DV028994
EST:     GCAGGATATGTCCCTATGGACTACAGGGAATATCTCAAAAAGATGTCAAA                         GAGTGGAGAATGGGGTGACCACGTTACATTGCAGGCTGCTGCAGACTCG
genomic: GCAGGATATGTCCCTATGGACTACAGGGAATATCTCAAAAAGATGTCAAAgtgagtattt ... attgaaccagGAGTGGAGAATGGGGTGACCACGTTACATTGCAGGCTGCTGCAGACTCG
EST: gi|71427953|gb|DR809003.1|DR809003
EST:     GCAGGATATGTCCCTATGGACTACAGGGAATATCTCAAAAAGATGTCAAA                         GAGTGGAGAATGGGGTGACCACGTTACATTGCAGGCTGCTGCAGACTCG
genomic: GCAGGATATGTCCCTATGGACTACAGGGAATATCTCAAAAAGATGTCAAAgtgagtattt ... attgaaccagGAGTGGAGAATGGGGTGACCACGTTACATTGCAGGCTGCTGCAGACTCG
EST: gi|166563741|gb|EG244809.1|EG244809
EST:     GGGAATATCTCAAAAAAGATGTCAAA                         GAGTGGAGAATGGGGTGACCACGTTACATTGCAGGCTGCTGCAGACTCG
genomic: GGGAATATCTC-AAAAAGATGTCAAAgtgagtattt ... attgaaccagGAGTGGAGAATGGGGTGACCACGTTACATTGCAGGCTGCTGCAGACTCG
EST: gi|86466720|gb|DY233090.1|DY233090
EST:     GCAGGATATGTCCCTATGGACTACAGGGAATATCTCAAAAAGATGTCAAA                         GAGTGGAGAATGGGGTGACCACGTTACATTGCAGGCTGCTGCAGACTCG
genomic: GCAGGATATGTCCCTATGGACTACAGGGAATATCTCAAAAAGATGTCAAAgtgagtattt ... attgaaccagGAGTGGAGAATGGGGTGACCACGTTACATTGCAGGCTGCTGCAGACTCG
EST: gi|71427180|gb|DR808230.1|DR808230
EST:     GCAGGATATGTCCCTATGGACTACAGGGAATATCTCAAAAAGATGTCAAA                         GAGTGGAGAATGGGGTGACCACGTTACATTGCAGGCTGCTGCAGACTCG
genomic: GCAGGATATGTCCCTATGGACTACAGGGAATATCTCAAAAAGATGTCAAAgtgagtattt ... attgaaccagGAGTGGAGAATGGGGTGACCACGTTACATTGCAGGCTGCTGCAGACTCG
EST: gi|50324081|gb|CO519207.1|CO519207
EST:     GCAGGATATGTCCCTATGGACTACAGGGAATATCTCAAAAAGATGTCAAA                         GAGTGGAGAATGGGGTGACCACGTTACATTGCAGGCTGCTGCAGACTCG
genomic: GCAGGATATGTCCCTATGGACTACAGGGAATATCTCAAAAAGATGTCAAAgtgagtattt ... attgaaccagGAGTGGAGAATGGGGTGACCACGTTACATTGCAGGCTGCTGCAGACTCG
EST: gi|50331811|gb|CO526937.1|CO526937
EST:     GCAGGATATGTCCCTATGGACTACAGGGAATATCTCAAAAAGATGTCAAA                         GAGTGGAGAATGGGGTGACCACGTTACATTGCAGGCTGCTGCAGACTCG
genomic: GCAGGATATGTCCCTATGGACTACAGGGAATATCTCAAAAAGATGTCAAAgtgagtattt ... attgaaccagGAGTGGAGAATGGGGTGACCACGTTACATTGCAGGCTGCTGCAGACTCG
EST: gi|78080763|gb|DV509175.1|DV509175
EST:     GCAGGATATGTCCCTATGGACTACAGGGAATATCTCAAAAAGATGTCAAA                         GAGTGGAGAATGGGGTGACCACGTTACATTGCAGGCTGCTGCAGACTCG
genomic: GCAGGATATGTCCCTATGGACTACAGGGAATATCTCAAAAAGATGTCAAAgtgagtattt ... attgaaccagGAGTGGAGAATGGGGTGACCACGTTACATTGCAGGCTGCTGCAGACTCG
EST: gi|50327716|gb|CO522842.1|CO522842
EST:     GCAGGATATGTCCCTATGGACTACAGGGAATATCTCAAAAAGATGTCAAA                         GAGTGGAGAATGGGGTGACCACGTTACATTGCAGGCTGCTGCAGACTCG
genomic: GCAGGATATGTCCCTATGGACTACAGGGAATATCTCAAAAAGATGTCAAAgtgagtattt ... attgaaccagGAGTGGAGAATGGGGTGACCACGTTACATTGCAGGCTGCTGCAGACTCG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

agtttataatctaaatatgcgtcctcattttgttatgcttaaacaattgaaccagGAGTGGAGAATGGGGTGACCACGTTACATTGCAGGCTGCTGCAGACTCG
        atctaaa  putative branch site (score: 3)
     ataatctaaatat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgagtatttgttccgctctccatttataatcaaatgtttagtttataatctaaatatgcgtcctcattttgttatgcttaaacaattgaaccagGAGTGGAGAATGGGGTGACCACGTTACATTGCAGGCTGCTGCAGACTCG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CTGCAG