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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgaaaaatattttcattttagttgtttaaatgacttgtgaaagacattgttaagtagatcatgccatgcgtgtagcacctaattgtaattactttgggtatagCCTTGCAAGGGAATATTGCTTTTTGGCCCCCCTGGCACAGGAAAAACAATGCTTGCAAAGGCTGTGGCAACTGAAGCTGGAGCAAATTTTATTAACATTT

Basic information

species Glycine max
transcript GLYMA02G17400.1
intron # 17
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA02G17400.1 (Glycine max), 3'ss of exon 17
lower sequence: LOC_Os11g43970.1 (Oryza sativa), 3'ss of exon 21
gtgaaaaatattttcattttagttgt---ttaaatgacttgtgaaagacattgt-taagtagatcatgccatgcgtgtagcacctaattgtaattactttgggtatagCCTTGCAAGGGAATATTGCTTTTTGGCCCCCCTGGCACAGGAAAAACAATGCTTGCAAAGGCTGTGGCAACTGAAGCTGGAGCAAATTTTATTAACATTT
       |||||||        | |    ||| |||     |     |  || | ||  ||  || |  | |     | ||  ||    |||| |   ||   |  |||||||||||||||||||||| ||||| || ||||| || || ||||| |||||||| ||||| || ||||||||||| || || || || |||||||| |
-----ctatattttgggacggatggagtattatatgttggctacctaattttctctatttaagtcctatcttaaaaattgcctctg---gtaaatctgttacttgcagCCTTGCAAGGGAATATTGCTGTTTGGACCTCCTGGTACTGGGAAAACCATGCTTGCTAAGGCAGTAGCAACTGAAGCAGGTGCTAACTTCATTAACATAT

upper sequence: GLYMA02G17400.1 (Glycine max), 3'ss of exon 17
lower sequence: LOC_Os03g22420.1 (Oryza sativa), 3'ss of exon 21
gtgaaaaatattttcattttagttgtttaaatgacttgtgaaagacattgttaagtagatcatgccatgcgtgtagcacctaattgtaattactttgggtat---agCCTTGCAAGGGAATATTGCTTTTTGGCCCCCCTGGCACAGGAAAAACAATGCTTGCAAAGGCTGTGGCAACTGAAGCTGGAGCAAATTTTATTAACATTT
|| |  |||   |     |      |||  ||     ||| ||    || ||    |  | ||   ||  ||| |    ||  |||| ||| |||  | | |   |||| || || |||||||| ||||||||||| ||||| |||||||| ||||||||||| || |||||||| || || ||||| || ||||| || || || |
gttatgaatggatgggggtactacttttggata----gtggaattttttatttc-cattttatttgata-gtgaactgactt-ttgttattgcttatgttgtgccagCCATGTAAAGGAATATTACTTTTTGGCCCGCCTGGTACAGGAAAGACAATGCTTGCCAAAGCTGTGGCTACAGAGGCTGGTGCGAATTTCATAAATATAT

upper sequence: GLYMA02G17400.1 (Glycine max), 3'ss of exon 17
lower sequence: LOC_Os07g47530.2 (Oryza sativa), 3'ss of exon 21
gtgaaaaatattttcattttagttgtttaaatgacttgtgaaagacattgttaagtagatcatgccatgcgtgtagca--cctaattgtaattac--tttgggtat-agCCTTGCAAGGGAATATTGCTTTTTGGCCCCCCTGGCACAGGAAAAACAATGCTTGCAAAGGCTGTGGCAACTGAAGCTGGAGCAAATTTTATTAACATTT
      |  ||  | ||| |  | || |   |   || |        |||||   |      | |||   || |  ||  | || || | || ||  |||    |  |||| || ||||||||||||||||||||||| ||||| || || || || |||||||| || ||||| ||||| || ||||| || |||||||| ||||| |
-----tagcatgctaattatcatggtctgttttttttatttggtctcttgtttctt----ttttccacttgtttcacaaacatagttctgatcaccatttattcaccagCCATGTAAGGGAATATTGCTTTTTGGCCCACCTGGTACGGGGAAGACCATGCTTGCTAAAGCTGTTGCAACAGAGGCTGGCGCCAATTTTATCAACATAT

upper sequence: GLYMA02G17400.1 (Glycine max), 3'ss of exon 17
lower sequence: GRMZM2G042074_T01 (Zea mays), 3'ss of exon 21
gtgaaaaatattttcattttagttgtttaaatgacttgtgaaagacattgttaagtagatcatgccatgcgtgtagcacctaattgtaattactttgggtatagCCTTGCAAGGGAATATTGCTTTTTGGCCCCCCTGGCACAGGAAAAACAATGCTTGCAAAGGCTGTGGCAACTGAAGCTGGAGCAAATTTTATTAACATTT
   |  |||||| | |||||       |||   |    || || |||   ||   ||| | |    | ||          |  || || |   ||       |||| || || ||||| || ||||||||||| ||||| || ||||| ||||||||||| ||||||||||||||||| ||||| || ||||| || ||||| |
-atagcaatattcttattttttgatgctaagctagcaatggaacacaccttt---tagctgacagaaagctaacttatgttgtttatattctattctataccagCCGTGTAAAGGAATTTTACTTTTTGGCCCACCTGGTACTGGAAAGACAATGCTTGCTAAGGCTGTGGCAACTGAGGCTGGTGCTAATTTCATAAACATAT

upper sequence: GLYMA02G17400.1 (Glycine max), 3'ss of exon 17
lower sequence: GRMZM2G126453_T02 (Zea mays), 3'ss of exon 6
gtgaaaaatattttcattttagttgtttaaatgacttgtgaaagacattgttaagtagatcatgccatgcgtgtagcacctaattgtaattactttgggtatagCCTTGCAAGGGAATATTGCTTTTTGGCCCCCCTGGCACAGGAAAAACAATGCTTGCAAAGGCTGTGGCAACTGAAGCTGGAGCAAATTTTATTAACATTT
     ||   |    || |    | || |||   | | || | ||  || || |     |   | || |    ||  ||    |    | | | ||   |  ||||||||||||| ||||||||||| || || |||||||| |||||||| |||||||| || || || ||||||||||| || || ||||| || || || |
---gtaatcttagatatgtcgagttttaaaacttcatctgta-gattttcttgacctactatagtcaagatcttataactgcctccgcaattcattctttgcagCCTTGCAAGGGGATATTGCTTTTCGGACCTCCTGGCACTGGAAAAACTATGCTTGCCAAAGCAGTAGCAACTGAAGCAGGCGCTAATTTCATCAATATAT

upper sequence: GLYMA02G17400.1 (Glycine max), 3'ss of exon 17
lower sequence: GRMZM2G052403_T01 (Zea mays), 3'ss of exon 12
gtgaaaaatattttcattttagttgt-ttaaatgacttg--tgaaagacattgttaa--gtagatcatgcc-atgcgtgtagcacctaattgtaattactttgggtatagCCTTGCAAGGGAATATTGCTTTTTGGCCCCCCTGGCACAGGAAAAACAATGCTTGCAAAGGCTGTGGCAACTGAAGCTGGAGCAAATTTTATTAACATTT
          |||  || ||||| || ||| ||   |||   |   || |   | ||  |||||| ||    |||      |  | | ||    | |   ||   |  ||||||||||||||||||||||||| || || |||||||| || ||||| |||||||| || || || ||||||||||| || || ||||| || || || |
----------tttgtatattagtagtgttagatatgttgggcgtttgaaaacttcaattgtagattattttgatgtactatggtcatgatccccaatttattctttgcagCCTTGCAAGGGAATATTGCTTTTCGGACCTCCTGGCACTGGGAAAACTATGCTTGCCAAAGCAGTAGCAACTGAAGCAGGTGCTAATTTCATCAATATAT

upper sequence: GLYMA02G17400.1 (Glycine max), 3'ss of exon 17
lower sequence: GRMZM2G435582_T01 (Zea mays), 3'ss of exon 1
gtgaaaaatattttcattttagttgtttaaatgacttgtgaaagacattgttaagtagatcatgccatgcgtgtagcacctaattgtaattactttgggtatagCCTTGCAAGGGAATATTGCTTTTTGGCCCCCCTGGCACAGGAAAAACAATGCTTGCAAAGGCTGTGGCAACTGAAGCTGGAGCAAATTTTATTAACATTT
     ||   |    || | ||   ||||||           |||  || || |     |   | || |    ||  ||    |  | | | | ||   |  ||||||||||||| ||||||||||| || || |||||||| |||||||| |||||||| || || || ||||||||||| || || ||||| || || || |
----taatcttagatatgtcagagttttaaaacttcatctgtagattttcttgacctactatggtcaagatcttataactgcctcctcaattcattctttgcagCCTTGCAAGGGGATATTGCTTTTCGGACCTCCTGGCACTGGAAAAACTATGCTTGCCAAAGCAGTAGCAACTGAAGCAGGCGCTAATTTCATCAATATAT

upper sequence: GLYMA02G17400.1 (Glycine max), 3'ss of exon 17
lower sequence: GRMZM2G157621_T03 (Zea mays), 3'ss of exon 21
-gtgaaaaatattttcattttagttgtttaaatgacttgtgaaagacattgttaagtagatcatgccatgcgtgtagcacctaattgtaattact--ttgggtatagCCTTGCAAGGGAATATTGCTTTTTGGCCCCCCTGGCACAGGAAAAACAATGCTTGCAAAGGCTGTGGCAACTGAAGCTGGAGCAAATTTTATTAACATTT
 ||||  |||  |   | |  |   |  ||   |       |    | | ||    | || || || |  | || |     |  || | || |    || |    |||| || || || |||||||||||||| || |||||||| || || || |||||||| || ||||| ||||| || ||||| || |||||||| ||||| |
agtgattaattgtccgagt--aaccgactagg-ggtcgactagtcgcctggtct--tcgaccaggcga--cttgaaatcattggttctgatcatctatttgccccagCCATGTAAAGGGATATTGCTTTTTGGTCCACCTGGCACCGGTAAGACCATGCTTGCCAAAGCTGTTGCAACAGAGGCTGGTGCTAATTTTATCAACATAT

upper sequence: GLYMA02G17400.1 (Glycine max), 3'ss of exon 17
lower sequence: GRMZM2G170037_T01 (Zea mays), 3'ss of exon 3
gtgaaaaatattttcattttagttgtttaaatgacttgtgaaagacattgttaagtagatcatgccatgcgtgtagcacctaattgtaattactttgggtatagCCTTGCAAGGGAATATTGCTTTTTGGCCCCCCTGGCACAGGAAAAACAATGCTTGCAAAGGCTGTGGCAACTGAAGCTGGAGCAAATTTTATTAACATTT
     ||   |    || | ||   ||||||           |||  || || |     |   | || |    ||  ||    |  | | | | ||   |  ||||||||||||| ||||||||||| ||  | |||||||| |||||||| |||||||| || || || |||||| |||  || || ||||| || || || |
----taatcttagatatgtcagagttttaaaacttcatctgtagattttcttgacctactatggtcaagatcttataactgcctcctcaattcattctttgcagCCTTGCAAGGGGATATTGCTTTTCGGATCTCCTGGCACTGGAAAAACTATGCTTGCCAAAGCAGTAGCAACTAAAGTAGGCGCTAATTTCATCAATATAT

upper sequence: GLYMA02G17400.1 (Glycine max), 3'ss of exon 17
lower sequence: Vv07s0005g00200.t01 (Vitis vinifera), 3'ss of exon 20
----------------------------------------gtgaaaa-atattttcattttagttg----tttaaatgacttgtgaaagacattgttaagtagatcatgccatgcgtgt--agcacctaattgtaattactttgggtatagCCTTGCAAGGGAATATTGCTTTTTGGCCCCCCTGGCACAGGAAAAACAATGCTTGCAAAGGCTGTGGCAACTGAAGCTGGAGCAAATTTTATTAACATTT
                                         |  | | ||||| |   | | || |    ||    ||| || || |||  | | |||  ||  ||||||| ||  |||  | || || | ||   ||||| |   |  ||||||||||||||||  | || ||||| || ||||| || ||||||||||||||||| ||||| || |||||||| || || ||||||||||| ||||| |
gttaggtgtttcacatgttttatttctttattgtgtatgtatatatatatattgtgtatctggtggaattttcttttgaattatggaagtaagttttatctaattcatgccttgtatgtctatcatctgaatgaggttactattttt-cagCCTTGCAAGGGAATTCTTCTATTTGGGCCTCCTGGGACTGGAAAAACAATGCTTGCGAAGGCGGTTGCAACTGAGGCAGGTGCAAATTTTATCAACATAT

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|120494480|gb|EH222647.1|EH222647
EST:     TGCTTCCTCTTCAAAGGCCTGAATTGTTTGGCAAAGGACAGCTGGCCAAG                         CCTTGCAAGGGAATATTGCTTTTTGGCCCCCCTGGCACAGGAAAAACAATG
genomic: TGCTTCCTCTTCAAAGGCCTGAATTGTTTGGCAAAGGACAGCTGGCCAAGgtgaaaaata ... ttgggtatagCCTTGCAAGGGAATATTGCTTTTTGGCCCCCCTGGCACAGGAAAAACAATG
EST: gi|16284522|gb|BI946134.1|BI946134
EST:     TGCTTCCTCTTCAAAGGCCTGAATTGTTTGGCAAAGGACAGCTGGCCAAG                         CCTTGCAAGGGAATATTGCTTTTTGGCCCCCCTGGCACAGGAAAAACAATG
genomic: TGCTTCCTCTTCAAAGGCCTGAATTGTTTGGCAAAGGACAGCTGGCCAAGgtgaaaaata ... ttgggtatagCCTTGCAAGGGAATATTGCTTTTTGGCCCCCCTGGCACAGGAAAAACAATG
EST: gi|120497089|gb|EH225256.1|EH225256
EST:     TGCTTCCTCTTCAAAGGCCTGAATTGTTTGGCAAAGGACAGCTGGCCAAG                         CCTTGCAAGGGAATATTGCTTTTTGGCCCCCCTGGCACAGGAAAAACAATG
genomic: TGCTTCCTCTTCAAAGGCCTGAATTGTTTGGCAAAGGACAGCTGGCCAAGgtgaaaaata ... ttgggtatagCCTTGCAAGGGAATATTGCTTTTTGGCCCCCCTGGCACAGGAAAAACAATG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gttaagtagatcatgccatgcgtgtagcacctaattgtaattactttgggtatagCCTTGCAAGGGAATATTGCTTTTTGGCCCCCCTGGCACAGGAAAAACAATGCTTGCAAAGGCTGTGGCAACTGAAGCTGGAGCAAATTTTATTAACATTT
                            acctaat  putative branch site (score: 3)
                                        ttacttt  putative PPT
                               taattgtaattacttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgaaaaatattttcattttagttgtttaaatgacttgtgaaagacattgttaagtagatcatgccatgcgtgtagcacctaattgtaattactttgggtatagCCTTGCAAGGGAATATTGCTTTTTGGCCCCCCTGGCACAGGAAAAACAATGCTTGCAAAGGCTGTGGCAACTGAAGCTGGAGCAAATTTTATTAACATTT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGCA