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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tccctaaattaattgaaattagaattactttattttaatttttaacctgtaaccaactaactggtctttattttttatttttcctaatcttcaattgcagCTGCTGATGTGCTCTTGTGGAGGAACAAGAAGATATCTGCTAGTGTACTTGGTGTAGCCACTGCTGTTTGGATCTTTTTTGAGTTGCTTGAATATCACCT

Basic information

species Glycine max
transcript GLYMA16G03410.1
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA16G03410.2 (Glycine max), 3'ss of exon 1
lower sequence: GRMZM2G159388_T01 (Zea mays), 3'ss of exon 1
--tccctaaa-ttaattga---aattagaattactttattttaatttttaacctgtaaccaactaactggtctttattttttatttttcctaatcttcaattgcagCTGCTGATGTGCTCTTGTGGAGGAACAAGAAGATATCTGCTAGTGTACTTGGTGTAGCCACTGCTGTTTGGATCTTTTTTGAGTTGCTTGAATATCACCT
  |   |||| || || ||   ||| ||||||     |  | |||   | | |      ||    ||    |  || |  |||   |||   || ||     | ||||||||||||| ||||||||||||||||||| || |||||| | ||||||||||  ||||| ||  | |||||||| ||||| |||||||  || || ||
gattgataaacttgatcgatgtaatgagaattgtgagacctaaataccttatcgtctgtcattgtaccca-caatactcattaccgttctctatttt-----gtagCTGCTGATGTGTTCTTGTGGAGGAACAAGAACATCTCTGCTGGAGTACTTGGTGGTGCCACAGCAATCTGGATCTTATTTGAATTGCTTGGCTACCATCT

upper sequence: GLYMA16G03410.2 (Glycine max), 3'ss of exon 1
lower sequence: GRMZM2G359018_T03 (Zea mays), 3'ss of exon 1
----tccctaaattaattgaaatta-gaattacttt-attttaatttttaacctgtaaccaactaactggtctttattttttatttttcctaatcttcaattgcagCTGCTGATGTGCTCTTGTGGAGGAACAAGAAGATATCTGCTAGTGTACTTGGTGTAGCCACTGCTGTTTGGATCTTTTTTGAGTTGCTTGAATATCACCT
    |   |    ||||   ||||  ||   |||   |  | |||   | | |      ||  | ||    ||| | |  ||| | |||   || ||     ||||||||||||||| || |||||||||||| ||| || || ||  | |||||||||| |||||| ||  | |||||| | ||||| |||||||  || || ||
gacttgattggtgtaatgtcaattgtgagacactgagacctaaatacctgatcgtctgtcattttacctacctt-actcattactcttctctatttt-----gcagCTGCTGATGTGTTCCTGTGGAGGAACAGGAACATCTCCGCCGGAGTACTTGGTGGAGCCACAGCAATCTGGATCCTATTTGAATTGCTTGGCTACCATCT

upper sequence: GLYMA16G03410.2 (Glycine max), 3'ss of exon 1
lower sequence: GRMZM2G359018_T02 (Zea mays), 3'ss of exon 1
tccctaaattaattgaaattagaattactttattttaatttttaacctgtaaccaactaactggtctttattttttatttttcctaatcttcaattgcagCTGCTGATGTGCTCTTGTGGAGGAACAAGAAGATATCTGCTAGTGTACTTGGTGTAGCCACTGCTGTTTGGATCTTTTTTGAGTTGCTTGAATATCACCT---------------------------------------------------------
                                                     ||  | ||    ||| | |  ||| | |||   || ||     ||||||||||||||| || |||||||||||| ||| || || ||  | |||||||||| |||||| ||  | |||||| | ||||| |||||||  || || ||                                                         
---------------------------------------------------gtcattttacctacctt-actcattactcttctctatttt-----gcagctgctgatgtgttcctgtggaggaacaggaacatctccgccggagtacttggtggagCCACAGCAATCTGGATCCTATTTGAATTGCTTGGCTACCATCTTCTTACTTTTGTTTGCCATGGTCTCATATTCTCTCTGGGTGTTCTCTTTCTCTGGTC

upper sequence: GLYMA16G03410.2 (Glycine max), 3'ss of exon 1
lower sequence: AT2G46170.2 (Arabidopsis thaliana), 3'ss of exon 1
-tccctaaattaattgaaattagaattact--ttattttaatttttaacctgtaaccaactaactggtctttattttttatttttcctaatcttcaattgcagCTGCTGATGTGCTCTTGTGGAGGAACAAGAAGATATCTGCTAGTGTACTTGGTGTAGCCACTGCTGTTTGGATCTTTTTTGAGTTGCTTGAATATCACCT
 |   | |||  | | ||||| |  ||| |  ||  ||   || || || | | |    || |  | |  | ||||||  | ||||  |||      ||||||||||||||||| ||||||||||| | || ||  |||| | |  ||| |||||||| || |||||| ||||| |  | || ||| || |||| |||||  |
ttgtatgaatgcaat-aaattggctttattggtttattatgttattgacttctgagtt-ctgagggattctgatttttc-tgtttctcaatgactctttgcagCTGCTGATGTGTTCTTGTGGAGGGATAAAAAACTATCAGGTGCTGTTCTTGGTGTCGCGACTGCTATTTGGGTTCTGTTCGAGCTGGTTGAGTATCATTT

upper sequence: GLYMA16G03410.2 (Glycine max), 3'ss of exon 1
lower sequence: Vv15s0046g01760.t01 (Vitis vinifera), 3'ss of exon 1
tccctaaattaattgaaattaga-attactttattttaatttttaacctgtaaccaactaactggtctttattttttatttttcc-taatcttcaattgcagCTGCTGATGTGCTCTTGTGGAGGAACAAGAAGATATCTGCTAGTGTACTTGGTGTAGCCACTGCTGTTTGGATCTTTTTTGAGTTGCTTGAATATCACCT
|   |   |||||  |  | ||  |||  ||| ||     | |   | ||   | ||||   |  ||||  |    | | || |  |  || |  | |||||  ||||||||  | |||||||||||||||||||| |||||  | |||||||| | |||||||||  | ||| |  |||| || ||||||||||| || ||
ttttttttttaatatatttgagggatttgtttgttccgggtctct-catgcc-ctaactttatcctcttcgtggggtttgttgctgtgttcatttaatgcagACGCTGATGTATTTTTGTGGAGGAACAAGAAGATCTCTGCCGGAGTACTTGGCGGAGCCACTGCCATGTGGGTGCTTTTCGAATTGCTTGAATACCATCT

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|12773506|gb|BG238433.1|BG238433
EST:     CCTCTTTGGAAGGGAGAAGCCAGTTCACTCCGTCCTCGGCGGTGGAAAAC                         CTGCTGATGTGCTCTTGTGGAGGAACAAGAAGATATCTGCTAGTGTACTTG
genomic: CCTCTTTGGAAGGGAGAAGCCAGTTCACTCCGTCCTCGGCGGTGGAAAACgtatgaattt ... tcaattgcagCTGCTGATGTGCTCTTGTGGAGGAACAAGAAGATATCTGCTAGTGTACTTG
EST: gi|13789319|gb|BG651910.1|BG651910
EST:     CCTCTTTGGAAGGGAGAAGCCAGTTCACTCCGTCCTCGGCGGTGGAAAAC                         CTGCTGATGTGCTCTTGTGGAGGAACAAGAAGATATCTGCTAGTGTACTTG
genomic: CCTCTTTGGAAGGGAGAAGCCAGTTCACTCCGTCCTCGGCGGTGGAAAACgtatgaattt ... tcaattgcagCTGCTGATGTGCTCTTGTGGAGGAACAAGAAGATATCTGCTAGTGTACTTG
EST: gi|298184383|gb|HO029596.1|HO029596
EST:     CCTCTTTGGAAGGGAGAAGCCAGTTCACTCCGTCCTCGGCGGTGGAAAAC                         CTGCTGATGTGCTCTTGTGGAGGAACAAGAAGATATCTGCTAGTGTACTTG
genomic: CCTCTTTGGAAGGGAGAAGCCAGTTCACTCCGTCCTCGGCGGTGGAAAACgtatgaattt ... tcaattgcagCTGCTGATGTGCTCTTGTGGAGGAACAAGAAGATATCTGCTAGTGTACTTG
EST: gi|16347651|gb|BI973246.1|BI973246
EST:     CCTCTTTGGAAGGGAGAAGCCAGTTCACTCCGTCCTCGGCGGTGGAAAAC                         CTGCTGATGTGCTCTTGTGGAGGAACAAGAAGATATCTGCTAGTGTACTTG
genomic: CCTCTTTGGAAGGGAGAAGCCAGTTCACTCCGTCCTCGGCGGTGGAAAACgtatgaattt ... tcaattgcagCTGCTGATGTGCTCTTGTGGAGGAACAAGAAGATATCTGCTAGTGTACTTG
EST: gi|9439799|gb|BE440313.1|BE440313
EST:     CCTCTTTGGAAGGGAGAAGCCAGTTCACTCCGTCCTCGGCGGTGGAAAAC                         CTGCTGATGTGCTCTTGTGGAGGAACAAGAAGATATCTGCTAGTGTACTTG
genomic: CCTCTTTGGAAGGGAGAAGCCAGTTCACTCCGTCCTCGGCGGTGGAAAACgtatgaattt ... tcaattgcagCTGCTGATGTGCTCTTGTGGAGGAACAAGAAGATATCTGCTAGTGTACTTG
EST: gi|19453060|gb|BM954470.1|BM954470
EST:     CCTCTTTGGAAGGGAGAAGCCAGTTCACTCCGTCCTCGGCGGTGGAAAAC                         CTGCTGATGTGCTCTTGTGGAGGAACAAGAAGATATCTGCTAGTGTACTTG
genomic: CCTCTTTGGAAGGGAGAAGCCAGTTCACTCCGTCCTCGGCGGTGGAAAACgtatgaattt ... tcaattgcagCTGCTGATGTGCTCTTGTGGAGGAACAAGAAGATATCTGCTAGTGTACTTG
EST: gi|9204464|gb|BE330688.1|BE330688
EST:     CCTCTTTGGAAGGGAGAAGCCAGTTCACTCCGTCCTCGGCGGTGGAAAAC                         CTGCTGATGTGCTCTTGTGGAGGAACAAGAAGATATCTGCTAGTGTACTTG
genomic: CCTCTTTGGAAGGGAGAAGCCAGTTCACTCCGTCCTCGGCGGTGGAAAACgtatgaattt ... tcaattgcagCTGCTGATGTGCTCTTGTGGAGGAACAAGAAGATATCTGCTAGTGTACTTG
EST: gi|192331495|gb|FK022742.1|FK022742
EST:     CCTCTTTGGAAGGGAGAAGCCAGTTCACTCCGTCCTCGGCGGTGGAAAAC                         CTGCTGATGTGCTCTTGTGGAGGAACAAGAAGATATCTGCTAGTGTACTTG
genomic: CCTCTTTGGAAGGGAGAAGCCAGTTCACTCCGTCCTCGGCGGTGGAAAACgtatgaattt ... tcaattgcagCTGCTGATGTGCTCTTGTGGAGGAACAAGAAGATATCTGCTAGTGTACTTG
EST: gi|151399497|gb|EV269368.1|EV269368
EST:     CCTCTTTGGAAGGGAGAAGCCAGTTCACTCCGTCCTCGGCGGTGGAAAAC                         CTGCTGATGTGCTCTTGTGGAGGAACAAGAAGATATCTGCTAGTGTACTTG
genomic: CCTCTTTGGAAGGGAGAAGCCAGTTCACTCCGTCCTCGGCGGTGGAAAACgtatgaattt ... tcaattgcagCTGCTGATGTGCTCTTGTGGAGGAACAAGAAGATATCTGCTAGTGTACTTG
EST: gi|19938446|gb|BQ081723.1|BQ081723
EST:     CCTCTTTGGAAGGGAGAAGCCAGTTCACTCCGTCCTCGGCGGTGGAAAAC                         CTGCTGATGTGCTCTTGTGGAGGAACAAGAAGATATCTGCTAGTGTACTTG
genomic: CCTCTTTGGAAGGGAGAAGCCAGTTCACTCCGTCCTCGGCGGTGGAAAACgtatgaattt ... tcaattgcagCTGCTGATGTGCTCTTGTGGAGGAACAAGAAGATATCTGCTAGTGTACTTG
EST: gi|151410252|gb|EV280067.1|EV280067
EST:     CCTCTTTGGAAGGGAGAAGCCAGTTCACTCCGTCCTCGGCGGTGGAAAAC                         CTGCTGATGTGCTCTTGTGGAGGAACAAGAAGATATCTGCTAGTGTACTTG
genomic: CCTCTTTGGAAGGGAGAAGCCAGTTCACTCCGTCCTCGGCGGTGGAAAACgtatgaattt ... tcaattgcagCTGCTGATGTGCTCTTGTGGAGGAACAAGAAGATATCTGCTAGTGTACTTG
EST: gi|192325969|gb|FK016646.1|FK016646
EST:     CCTCTTTGGAAGGGAGAAGCCAGTTCACTCCGTCCTCGGCGGTGGAAAAC                         CTGCTGATGTGCTCTTGTGGAGGAACAAGAAGATATCTGCTAGTGTACTTG
genomic: CCTCTTTGGAAGGGAGAAGCCAGTTCACTCCGTCCTCGGCGGTGGAAAACgtatgaattt ... tcaattgcagCTGCTGATGTGCTCTTGTGGAGGAACAAGAAGATATCTGCTAGTGTACTTG
EST: gi|22524798|gb|BU083609.1|BU083609
EST:     CCTCTTTGGAAGGGAGAAGCCAGTTCACTCCGTCCTCGGCGGTGGAAAAC                         CTGCTGATGTGCTCTTGTGGAGGAACAAGAAGATATCTGCTAGTGTACTTG
genomic: CCTCTTTGGAAGGGAGAAGCCAGTTCACTCCGTCCTCGGCGGTGGAAAACgtatgaattt ... tcaattgcagCTGCTGATGTGCTCTTGTGGAGGAACAAGAAGATATCTGCTAGTGTACTTG
EST: gi|18040508|gb|BM308802.1|BM308802
EST:     CCTCTTTGGAAGGGAGAAGCCAGTTCACTCCGTCCTCGGCGGTGGAAAAC                         CTGCTGATGTGCTCTTGTGGAGGAACAAGAAGATATCTGCTAGTGTACTTG
genomic: CCTCTTTGGAAGGGAGAAGCCAGTTCACTCCGTCCTCGGCGGTGGAAAACgtatgaattt ... tcaattgcagCTGCTGATGTGCTCTTGTGGAGGAACAAGAAGATATCTGCTAGTGTACTTG
EST: gi|26048778|gb|CA785231.1|CA785231
EST:     CCTCTTTGGAAGGGAGAAGCCAGTTCACTCCGTCCTCGGCGGTGGAAAAC                         CTGCTGATGTGCTCTTGTGGAGGAACAAGAAGATATCTGCTAGTGTACTTG
genomic: CCTCTTTGGAAGGGAGAAGCCAGTTCACTCCGTCCTCGGCGGTGGAAAACgtatgaattt ... tcaattgcagCTGCTGATGTGCTCTTGTGGAGGAACAAGAAGATATCTGCTAGTGTACTTG
EST: gi|192294452|gb|FG987381.1|FG987381
EST:     CCTCTTTGGAAGGGAGAAGCCAGTTCACTCCGTCCTCGGCGGTGGAAAAC                         CTGCTGATGTGCTCTTGTGGAGGAACAAGAAGATATCTGCTAGTGTACTTG
genomic: CCTCTTTGGAAGGGAGAAGCCAGTTCACTCCGTCCTCGGCGGTGGAAAACgtatgaattt ... tcaattgcagCTGCTGATGTGCTCTTGTGGAGGAACAAGAAGATATCTGCTAGTGTACTTG
EST: gi|7458579|gb|AW666029.1|AW666029
EST:     CCTCTTTGGAAGGGAGAAGCCAGTTCACTCCGTCCTCGGCGGTGGAAAAC                         CTGCTGATGTGCTCTTGTGGAGGAACAAGAAGATATCTGCTAGTGTACTTG
genomic: CCTCTTTGGAAGGGAGAAGCCAGTTCACTCCGTCCTCGGCGGTGGAAAACgtatgaattt ... tcaattgcagCTGCTGATGTGCTCTTGTGGAGGAACAAGAAGATATCTGCTAGTGTACTTG
EST: gi|23050778|gb|BU577030.1|BU577030
EST:     CCTCTTTGGAAGGGAGAAGCCAGTTCACTCCGTCCTCGGCGGTGGAAAAC                         CTGCTGATGTGCTCTTGTGGAGGAACAAGAAGATATCTGCTAGTGTACTTG
genomic: CCTCTTTGGAAGGGAGAAGCCAGTTCACTCCGTCCTCGGCGGTGGAAAACgtatgaattt ... tcaattgcagCTGCTGATGTGCTCTTGTGGAGGAACAAGAAGATATCTGCTAGTGTACTTG
EST: gi|16347591|gb|BI973186.1|BI973186
EST:     CCTCTTTGGAAGGGAGAAGCCAGTTCACTCCGTCCTCGGCGGTGGAAAAC                         CTGCTGATGTGCTCTTGTGGAGGAACAAGAAGATATCTGCTAGTGTACTTG
genomic: CCTCTTTGGAAGGGAGAAGCCAGTTCACTCCGTCCTCGGCGGTGGAAAACgtatgaattt ... tcaattgcagCTGCTGATGTGCTCTTGTGGAGGAACAAGAAGATATCTGCTAGTGTACTTG
EST: gi|151393790|gb|EV263665.1|EV263665
EST:     CCTCTTTGGAAGGGAGAAGCCAGTTCACTCCGTCCTCGGCGGTGGAAAAC                         CTGCTGATGTGCTCTTGTGGAGGAACAAGAAGATATCTGCTAGTGTACTTG
genomic: CCTCTTTGGAAGGGAGAAGCCAGTTCACTCCGTCCTCGGCGGTGGAAAACgtatgaattt ... tcaattgcagCTGCTGATGTGCTCTTGTGGAGGAACAAGAAGATATCTGCTAGTGTACTTG
EST: gi|192300856|gb|FG991178.1|FG991178
EST:     CCTATTTGGAAGGGAGAAGCCAGTTCACTCCGTCCTCGGCGGTGGAAAAC                         CTGCTGATGTGCTCTTGTGGAGGAACAAGAAGATATCTGCTAGTGTACTTG
genomic: CCTCTTTGGAAGGGAGAAGCCAGTTCACTCCGTCCTCGGCGGTGGAAAACgtatgaattt ... tcaattgcagCTGCTGATGTGCTCTTGTGGAGGAACAAGAAGATATCTGCTAGTGTACTTG
EST: gi|57575716|gb|CX548691.1|CX548691
EST:     GGCGGTGGAAAAC                         CTGCTGATGTGCTCTTGTGGAGGAACAAGAAGATATCTGCTAGTGTACTTG
genomic: GGCGGTGGAAAACgtatgaattt ... tcaattgcagCTGCTGATGTGCTCTTGTGGAGGAACAAGAAGATATCTGCTAGTGTACTTG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cctgtaaccaactaactggtctttattttttatttttcctaatcttcaattgcagCTGCTGATGTGCTCTTGTGGAGGAACAAGAAGATATCTGCTAGTGTACTTGGTGTAGCCACTGCTGTTTGGATCTTTTTTGAGTTGCTTGAATATCACCT
                   tctttattttttattt  CT-rich tract
                     tttattttttattttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tccctaaattaattgaaattagaattactttattttaatttttaacctgtaaccaactaactggtctttattttttatttttcctaatcttcaattgcagCTGCTGATGTGCTCTTGTGGAGGAACAAGAAGATATCTGCTAGTGTACTTGGTGTAGCCACTGCTGTTTGGATCTTTTTTGAGTTGCTTGAATATCACCT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGTT
-ccctaaa
- - - - - - - - - - - - - - - - - - - - - - acctgta
- - - - - - - - - - - - - - - - - - - - - - - - - - ccaacta