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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tgttctggaactggaattagctgtgtagtgtaatatgggattagctttatttattttactcattgtttgatcttcccctatatatttctttgccgtacagGTATGAGAACATGGACATCGCTTTACATTATGGTGCTATGTTGAGGGAATGTATTCGCCACCAAAGCATTGCAAG

Basic information

species Zea mays
transcript GRMZM2G066051_T01
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G066051_T01 (Zea mays), 3'ss of exon 3
lower sequence: LOC_Os07g39630.1 (Oryza sativa), 3'ss of exon 3
-tgttctggaactggaattagctgtgtagtgtaatatgggattagctttatttatttt-actcattgtttgatcttcccctatatatttctttgccgtacagGTATGAGAACATGGACATCGCTTTACATTATGGTGCTATGTTGAGGGAATGTATTCGCCACCAAAGCATTGCAAG
  ||      |     |||   |    | | |    |  |  || | |||||  ||   |||   | |      ||  ||| |   ||||  | |    |||||||||||| |||||||| ||||| ||||| ||  ||||| ||||||||||||||||||||||||| ||||||||
cagtagccacatgattattgcattccaaatatttcttatg--taccgttattgcttcagactagctttgcttattttgcctgttattttcactacttaccagGTATGAGAATATGGACATTGCTTTGCATTACGGCTCTATGCTGAGGGAATGTATTCGCCACCAAAGTATTGCAAG

upper sequence: GRMZM2G066051_T01 (Zea mays), 3'ss of exon 3
lower sequence: AT5G47540.1 (Arabidopsis thaliana), 3'ss of exon 3
-tgttctggaactggaattagctgtgtagtg--taatatgggattagctttatttattttactcattgtttgatcttcccctatatatttctttgccgta---cagGTATGAGAACATGGACATCGCTTTACATTATGGTGCTATGTTGAGGGAATGTATTCGCCACCAAAGCATTGCAAG
 ||         ||  | || |  || |||   || |  |   ||      | |||    |  |    ||| ||| |    ||||  ||||  ||   |    ||| |  |||||||  ||||| |||||||| |||||||||||||| ||||| ||||| || || || |   | || | 
gtgagtcttgtgtgttactatcattgaagttattagttggtagtttttccaaattaagagataccacattttatcatttt-tatagctttccatgttttgtgtcagCTTCGAGAACACAGACATGGCTTTACACTATGGTGCTATGTTTAGGGAGTGTATCCGTCATCAGATTGTGGCTAA

upper sequence: GRMZM2G066051_T01 (Zea mays), 3'ss of exon 3
lower sequence: Vv19s0090g01550.t01 (Vitis vinifera), 3'ss of exon 3
tgttctggaactggaattagctgtgtagtgtaatatgggattagctttatttatttt--actcattgtttg-atcttcccctatatatttctttgc-cgtacagGTATGAGAACATGGACATCGCTTTACATTATGGTGCTATGTTGAGGGAATGTATTCGCCACCAAAGCATTGCAAG
 | | | ||||| | || |    || ||  || |  |  |||   |||||  || ||   || |||  ||| |   |    |   |||         | |  ||||||||| |  ||||||| ||||||||||||||||  |||||||  || || || ||||| || |||||||||||
-gcttttgaactagcatcat---tggagaatatttagacattctatttatcaatcttcagcttattacttgtaaaatatattgcttatcatggaattcctttagGTATGAGGATCTGGACATTGCTTTACATTATGGTGGAATGTTGAAAGAGTGCATACGCCATCAGAGCATTGCAAG

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|149041352|gb|EE046990.2|EE046990
EST:     TCTGAGTACCTAGAGTCAAATAAAGATCTCTTGGACATTTTAATTTTAGG                         GTATGAGAACATGGACATCGCTTTACATTATGGTGCTATGTTGAGGGAAT
genomic: TCTGAGTACCTAGAGTCAAATAAAGATCTCTTGGACATTTTAATTTTAGGgtaagactac ... tgccgtacagGTATGAGAACATGGACATCGCTTTACATTATGGTGCTATGTTGAGGGAAT
EST: gi|148999214|gb|EE036133.2|EE036133
EST:     TCTGAGTACCTAGAGTCAAATAAAGATCTCTTGGACATTTTAATTTTAGG                         GTATGAGAACATGGACATCGCTTTACATTATGGTGCTATGTTGAGGGAATG
genomic: TCTGAGTACCTAGAGTCAAATAAAGATCTCTTGGACATTTTAATTTTAGGgtaagactac ... tgccgtacagGTATGAGAACATGGACATCGCTTTACATTATGGTGCTATGTTGAGGGAATG
EST: gi|78107219|gb|DV525637.1|DV525637
EST:     TCTGAGTACCTAGAGTCAAATAAAGATCTCTTGGACATTTTAATTTTAGG                         GTATGAGAACATGGACATCGCTTTACATTATGGTGCTATGTTGAGGGAATG
genomic: TCTGAGTACCTAGAGTCAAATAAAGATCTCTTGGACATTTTAATTTTAGGgtaagactac ... tgccgtacagGTATGAGAACATGGACATCGCTTTACATTATGGTGCTATGTTGAGGGAATG
EST: gi|149072876|gb|EE161132.2|EE161132
EST:     TCTGAGTACCTAGAGTCAAATAAAGATCTCTTGGACATTTTAATTTTAGG                         GTATGAGAACATGGACATCGCTTTACATTATGGTGCTATGTTGAGGGAATG
genomic: TCTGAGTACCTAGAGTCAAATAAAGATCTCTTGGACATTTTAATTTTAGGgtaagactac ... tgccgtacagGTATGAGAACATGGACATCGCTTTACATTATGGTGCTATGTTGAGGGAATG
EST: gi|18660671|gb|BM500986.1|BM500986
EST:     CTCTTGGACATTTTAATTTTAGG                         GTATGAGAACATGGACATCGCTTTACATTATGGTGCTATGTTGAGGGAATG
genomic: CTCTTGGACATTTTAATTTTAGGgtaagactac ... tgccgtacagGTATGAGAACATGGACATCGCTTTACATTATGGTGCTATGTTGAGGGAATG
EST: gi|7844268|gb|AW787490.1|AW787490
EST:     TCTGAGTACCTAGAGTCAAATAAAGATCTCTTGGACATTTTAATTTTAGG                         GTATGAGAACATGGACATCGCTTTACATTATGGTGCTATGTTGAGGGAATG
genomic: TCTGAGTACCTAGAGTCAAATAAAGATCTCTTGGACATTTTAATTTTAGGgtaagactac ... tgccgtacagGTATGAGAACATGGACATCGCTTTACATTATGGTGCTATGTTGAGGGAATG
EST: gi|6194845|gb|AW146949.1|AW146949
EST:     TCTGAGTACCTAGAGTCAAATAAAGATCTCTTGGACATTTTAATTTTAGG                         GTATGAGAACATGGACATCGCTTTACATTATGGTGCTATGTTGAGGGAATG
genomic: TCTGAGTACCTAGAGTCAAATAAAGATCTCTTGGACATTTTAATTTTAGGgtaagactac ... tgccgtacagGTATGAGAACATGGACATCGCTTTACATTATGGTGCTATGTTGAGGGAATG
EST: gi|211268420|gb|FL369229.1|FL369229
EST:     TCTGAGTACCTAGAGTCAAATAAAGATCTCTTGGACATTTTAATTTTAGG                         GTATGAGAACATGGACATCGCTTTACATTATGGTGCTATGTTGAGGGAATG
genomic: TCTGAGTACCTAGAGTCAAATAAAGATCTCTTGGACATTTTAATTTTAGGgtaagactac ... tgccgtacagGTATGAGAACATGGACATCGCTTTACATTATGGTGCTATGTTGAGGGAATG
EST: gi|71447694|gb|DR828744.1|DR828744
EST:     TCTGAGTACCTAGAGTCAAATAAAGATCTCTTGGACATTTTAATTTTAGG                         GTATGAGAACATGGACATCGCTTTACATTATGGTGCTATGTTGAGGGAATG
genomic: TCTGAGTACCTAGAGTCAAATAAAGATCTCTTGGACATTTTAATTTTAGGgtaagactac ... tgccgtacagGTATGAGAACATGGACATCGCTTTACATTATGGTGCTATGTTGAGGGAATG
EST: gi|148955827|gb|EC901514.2|EC901514
EST:     TCTGAGTACCTAGAGTCAAATAAAGATCTCTTGGACATTTTAATTTTAGG                         GTATGAGAACATGGACATCGCTTTACATTATGGTGCTATGTTGAGGGAATG
genomic: TCTGAGTACCTAGAGTCAAATAAAGATCTCTTGGACATTTTAATTTTAGGgtaagactac ... tgccgtacagGTATGAGAACATGGACATCGCTTTACATTATGGTGCTATGTTGAGGGAATG
EST: gi|71328881|gb|DR801123.1|DR801123
EST:     TCTGAGTACCTAGAGTCAAATAAAGATCTCTTGGACATTTTAATTTTAGG                         GTATGAGAACATGGACATCGCTTTACATTATGGTGCTATGTTGAGGGAATG
genomic: TCTGAGTACCTAGAGTCAAATAAAGATCTCTTGGACATTTTAATTTTAGGgtaagactac ... tgccgtacagGTATGAGAACATGGACATCGCTTTACATTATGGTGCTATGTTGAGGGAATG
EST: gi|31354689|gb|CD439046.1|CD439046
EST:     TCTGAGTACCTAGAGTCAAATAAAGATCTCTTGGACATTTTAATTTTAGG                         GTATGAGAACATGGACATCGCTTTACATTATGGTGCTATGTTGAGGGAATG
genomic: TCTGAGTACCTAGAGTCAAATAAAGATCTCTTGGACATTTTAATTTTAGGgtaagactac ... tgccgtacagGTATGAGAACATGGACATCGCTTTACATTATGGTGCTATGTTGAGGGAATG
EST: gi|60340162|gb|DN207135.1|DN207135
EST:     TCTGAGTACCTAGAGTCAAATAAAGATCTCTTGGACATTTTAATTTTAGG                         GTATGAGAACATGGACATCGCTTTACATTATGGTGCTATGTTGAGGGAAT
genomic: TCTGAGTACCTAGAGTCAAATAAAGATCTCTTGGACATTTTAATTTTAGGgtaagactac ... tgccgtacagGTATGAGAACATGGACATCGCTTTACATTATGGTGCTATGTTGAGGGAAT
EST: gi|32856027|gb|CD995708.1|CD995708
EST:     TCTGAGTACCTAGAGTCAAATAAAGATCTCTTGGACATTTTAATTTTAGG                         GTATGAGAACATGGACATCGCTTTACATTATGGTGCTATGTTGAGGGAATG
genomic: TCTGAGTACCTAGAGTCAAATAAAGATCTCTTGGACATTTTAATTTTAGGgtaagactac ... tgccgtacagGTATGAGAACATGGACATCGCTTTACATTATGGTGCTATGTTGAGGGAATG
EST: gi|149082296|gb|EE171481.2|EE171481
EST:     TCTGAGTACCTAGAGTCAAATAAAGATCTCTTGGACATTTTAATTTTAGG                         GTATGAGAACATGGACATCGCTTTACATTATGGTGCTATGTTGAGGGGATG
genomic: TCTGAGTACCTAGAGTCAAATAAAGATCTCTTGGACATTTTAATTTTAGGgtaagactac ... tgccgtacagGTATGAGAACATGGACATCGCTTTACATTATGGTGCTATGTTGAGGGAATG
EST: gi|6994177|gb|AW453391.1|AW453391
EST:     TCTGAGTACCTAGAGTCAAATAAAGATCTCTTGGACATTTTAATTTTAGG                         GTATGAGAACATGGACATCGCTTTACATTATGGTGCTATGTTGAGGGAATG
genomic: TCTGAGTACCTAGAGTCAAATAAAGATCTCTTGGACATTTTAATTTTAGGgtaagactac ... tgccgtacagGTATGAGAACATGGACATCGCTTTACATTATGGTGCTATGTTGAGGGAATG
EST: gi|7844267|gb|AW787489.1|AW787489
EST:     TCTGAGTACCTAGAGTCAAATAAAGATCTCTTGGACATTTTAATTTTAGG                         GTATGAGAACATGGACATCGCTTTACATTATGGTGCTATGTTGAGGGAATG
genomic: TCTGAGTACCTAGAGTCAAATAAAGATCTCTTGGACATTTTAATTTTAGGgtaagactac ... tgccgtacagGTATGAGAACATGGACATCGCTTTACATTATGGTGCTATGTTGAGGGAATG
EST: gi|6022524|gb|AW067557.1|AW067557
EST:     TCTGAGTACCTAGAGTCAAATAAAGATCTCTTGGACATTTTAATTTTAGG                         GTATGAGAACATGGACATCGCTTTACATTATGGTGCTATGTTGAGGGAATG
genomic: TCTGAGTACCTAGAGTCAAATAAAGATCTCTTGGACATTTTAATTTTAGGgtaagactac ... tgccgtacagGTATGAGAACATGGACATCGCTTTACATTATGGTGCTATGTTGAGGGAATG
EST: gi|6445388|gb|AW179351.1|AW179351
EST:     TCTGAGTACCTAGAGTCAAATAAAGATCTCTTGGACATTTTAATTTTAGG                         GTATGAGAACATGGACATCGCTTTACATTATGGTGCTATGTTGAGGGAATG
genomic: TCTGAGTACCTAGAGTCAAATAAAGATCTCTTGGACATTTTAATTTTAGGgtaagactac ... tgccgtacagGTATGAGAACATGGACATCGCTTTACATTATGGTGCTATGTTGAGGGAATG
EST: gi|6056599|gb|AW091004.1|AW091004
EST:     GTCAAATAAAGATCTCTTGGACATTTTAATTTTAGG                         GTATGAGAACATGGACATCGCTTTACATTATGGTGCTATGTTGAGGGAATG
genomic: GTCAAATAAAGATCTCTTGGACATTTTAATTTTAGGgtaagactac ... tgccgtacagGTATGAGAACATGGACATCGCTTTACATTATGGTGCTATGTTGAGGGAATG
EST: gi|149079796|gb|EE168794.2|EE168794
EST:     TCTGAGTACCTAGAGTCAAATAAAGATCTCTTGGACATTTTAATTTTAGG                         GTATGAGAACATGGACATCGCTTTACATTATGGTGCTATGTTGAGGGGATG
genomic: TCTGAGTACCTAGAGTCAAATAAAGATCTCTTGGACATTTTAATTTTAGGgtaagactac ... tgccgtacagGTATGAGAACATGGACATCGCTTTACATTATGGTGCTATGTTGAGGGAATG
EST: gi|149013854|gb|EE043335.2|EE043335
EST:     TCTGAGTACCTAGAGTCAAATAAAGATCTCTTGGACATTTTAATTTTAGG                         GTATGAGAACATGGACATCGCTTTACATTATGGTGCTATGTTGAGGGAATG
genomic: TCTGAGTACCTAGAGTCAAATAAAGATCTCTTGGACATTTTAATTTTAGGgtaagactac ... tgccgtacagGTATGAGAACATGGACATCGCTTTACATTATGGTGCTATGTTGAGGGAATG

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), 47 (downstream exon)
Score: 215

AAGTTGTTGCAAACTTGCAAAGACAGCAAGTATCCTCAAAGATAGTAGCGTCTGAGTACCTAGAGTCAAATAAAGATCTCTTGGACATTTTAATTTTAGGgtaagactac ... tgccgtacagGTATGAGAACATGGACATCGCTTTACATTATGGTGCTATGTTGAGGGAATGTATTCGCCACCAAAGCATTGCAAG


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 321

AAGTTGTTGCAAACTTGCAAAGACAGCAAGTATCCTCAAAGATAGTAGCGTCTGAGTACCTAGAGTCAAATAAAGATCTCTTGGACATTTTAATTTTAGGgtaagactac ... tgccgtacagGTATGAGAACATGGACATCGCTTTACATTATGGTGCTATGTTGAGGGAATGTATTCGCCACCAAAGCATTGCAAG


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 218

AAGTTGTTGCAAACTTGCAAAGACAGCAAGTATCCTCAAAGATAGTAGCGTCTGAGTACCTAGAGTCAAATAAAGATCTCTTGGACATTTTAATTTTAGGgtaagactac ... tgccgtacagGTATGAGAACATGGACATCGCTTTACATTATGGTGCTATGTTGAGGGAATGTATTCGCCACCAAAGCATTGCAAG


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 271

AAGTTGTTGCAAACTTGCAAAGACAGCAAGTATCCTCAAAGATAGTAGCGTCTGAGTACCTAGAGTCAAATAAAGATCTCTTGGACATTTTAATTTTAGGgtaagactac ... tgccgtacagGTATGAGAACATGGACATCGCTTTACATTATGGTGCTATGTTGAGGGAATGTATTCGCCACCAAAGCATTGCAAG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tttatttattttactcattgtttgatcttcccctatatatttctttgccgtacagGTATGAGAACATGGACATCGCTTTACATTATGGTGCTATGTTGAGGGAATGTATTCGCCACCAAAGCATTGCAAG
                   gtttgat  putative branch site (score: 271)
                         tcttcccctatatatt  CT-rich tract
                                 tatatatttcttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tgttctggaactggaattagctgtgtagtgtaatatgggattagctttatttattttactcattgtttgatcttcccctatatatttctttgccgtacagGTATGAGAACATGGACATCGCTTTACATTATGGTGCTATGTTGAGGGAATGTATTCGCCACCAAAGCATTGCAAG

tgttctg
- - - - - - - - - agctgtg