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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagttggaaagctcctgtggttgagctaacctctctccctctccccctctttttctctaggcattctcaaataatcatattatgatttcagGAATAACAAGAGATGGTTTATTAATGAGAATGAAGAAATCTCAATGGCAGGATGTTATTGATCTAAATCTCACTGGTGTTTTTCTTTGCACACAG

Basic information

species Glycine max
transcript GLYMA18G01280.1
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA18G01280.1 (Glycine max), 3'ss of exon 5
lower sequence: LOC_Os04g30760.1 (Oryza sativa), 3'ss of exon 5
gtaagttggaaagctcctgtggttgagctaacctctctccctctccccctc-tttttctctaggcattctcaaat---aatcatattatgatttcagGAATAACAAGAGATGGTTTATTAATGAGAATGAAGAAATCTCAATGGCAGGATGTTATTGATCTAAATCTCACTGGTGTTTTTCTTTGCACACAG
||  |     |   |  | |  ||    ||   | | |    || ||  || | ||  || |    |    ||||   ||  | ||  || | |||||||| ||  ||||    ||||||||||| ||||||||||| |||||||| || || ||||| || ||||| ||||||||||| || || ||||| 
gttgggccccattgtagtttcatttctttacattttttttagcttcctatcatgttaatcaatttgtctgtaaattaaaagaacatcttgttatcagGAATTACCCGAGACACATTATTAATGAGGATGAAGAAATCACAATGGCAAGACGTAATTGACCTGAATCTTACTGGTGTTTTCCTCTGTACACAA

upper sequence: GLYMA18G01280.1 (Glycine max), 3'ss of exon 5
lower sequence: LOC_Os02g30060.1 (Oryza sativa), 3'ss of exon 5
gtaagttggaaagctcct-gtggttgagctaacctctctccctctcc-------ccctctttttctctaggcattctcaaataatcatattatgat-ttcagGAATAACAAGAGATGGTTTATTAATGAGAATGAAGAAATCTCAATGGCAGGATGTTATTGATCTAAATCTCACTGGTGTTTTTCTTTGCACACAG
             ||||| ||||   |    | || | |    | |        |  | | |||  ||    | | | ||        ||| |||| ||||||||| ||| | |||   || ||  ||||||||||||||||||| ||||| |||||  ||||||| ||||| || || || || ||||||||||||
----------gtactcctagtggaatattatatcttttttttacacaaaaaaaacaatttattttacttttaagttttaaccctgaccattctgatattcagGAATCACACGGGATACATTGTTGCTGAGAATGAAGAAATCTCAGTGGCAAGATGTAGTTGATCTTAATCTTACGGGCGTATTCCTTTGCACACAG

upper sequence: GLYMA18G01280.1 (Glycine max), 3'ss of exon 5
lower sequence: GRMZM2G351023_T01 (Zea mays), 3'ss of exon 5
gtaagttggaaagctcctgtggttgagctaacctctctccctctccccctctttttctctaggcattctcaaataatca-tattatgatttcagGAATAACAAGAGATGGTTTATTAATGAGAATGAAGAAATCTCAATGGCAGGATGTTATTGATCTAAATCTCACTGGTGTTTTTCTTTGCACACAG
        | | | |||  || | ||    || |  |   |||      |  ||  || |     ||  ||||||| || |||| |  | | |||||| ||| ||||    ||||| ||||| |||||||||||||| ||||| ||||| |||||||| ||||| || || || |  || || ||||||
--------gtatgttcccatgttagattgcactttgccagctccttgtttgattgactttgt---ttggcaaataaacaatattttcttattagGAATTACACGAGACACATTATTGATGAGGATGAAGAAATCTCAGTGGCAAGATGTAATTGATCTGAATCTTACAGGCGTCTGCCTGTGTACACAG

upper sequence: GLYMA18G01280.1 (Glycine max), 3'ss of exon 5
lower sequence: GRMZM2G099696_T01 (Zea mays), 3'ss of exon 5
gtaagttggaaagctcctgtggttgagctaacctctctccctctccccctctttttctctaggcattc----tcaaataatca-tattatgatttcagGAATAACAAGAGATGGTTTATTAATGAGAATGAAGAAATCTCAATGGCAGGATGTTATTGATCTAAATCTCACTGGTGTTTTTCTTTGCACACAG
||| |||   ||  |||  ||||  |    || |  |    || | |   |   ||   | | | ||     |||||||| || |||| |  | | ||| || ||| ||||    || || ||||| |||||||||||||| ||||| || || |||||||| ||||| ||||| || || ||||| ||||||
gtatgttctcaacttcccatggtatattgcactttgccagttcccacttcccagtttggttgactttgtttgtcaaataaacaatattttcttattagGGATTACACGAGACACATTGTTGATGAGGATGAAGAAATCTCAGTGGCAAGACGTAATTGATCTGAATCTTACTGGCGTCTTCCTTTGTACACAG

upper sequence: GLYMA18G01280.1 (Glycine max), 3'ss of exon 5
lower sequence: GRMZM2G043602_T03 (Zea mays), 3'ss of exon 4
gtaagttggaaagctcctgtggttgagctaacctctctccctctccc-cctctttttctctaggcattctcaaataatcatattatgatttcagGAATAACAAGAGATGGTTTATTAATGAGAATGAAGAAATCTCAATGGCAGGATGTTATTGATCTAAATCTCACTGGTGTTTTTCTTTGCACACAG
           |   ||  |  ||    | |  |  |  |  || |    | |||  ||     || | |  |  ||  |  | || ||   |||||| ||| | ||    || || ||||||||||||||||| || ||||| ||||| |||||| | ||||| || || ||||| |||||||| |||
---------gtaatgccaattattattattattttgcaactactacaatttgtttcacttccaacaat-tggagcaaaaaactgataat---agGAATCACACGGGACACATTGTTGATGAGAATGAAGAAATCACAGTGGCAAGATGTGATTGATTTGAATCTTACAGGCGTTTTCCTTTGCACGCAG

upper sequence: GLYMA18G01280.1 (Glycine max), 3'ss of exon 5
lower sequence: Vv01s0010g02670.t01 (Vitis vinifera), 3'ss of exon 5
gtaagttggaaagctcctgtggttgag--ctaacctctctccctctccccctctttttctctaggcattctcaaataatca---tattatgatttcagGAATAACAAGAGATGGTTTATTAATGAGAATGAAGAAATCTCAATGGCAGGATGTTATTGATCTAAATCTCACTGGTGTTTTTCTTTGCACACAG
                  || |||||    | |||||  |   | |    ||   |   |  |  | || || | |||      || |||| |||||||||| ||  | ||||| || || ||||||||||||| | | ||||||||||| || ||| || | |||||||| ||||| || || |||||||||
------------------gttgttgaaacttgacctccttttttttgtagcttactagtttcaaactttgtccactaactgatctactatggtttcagGAATTACTCGGGATGGGTTGTTGATGAGAATGAAGACACCACAATGGCAGGAGGTCATTAATTTGAATCTCACAGGTGTATTCCTCTGCACACAG

upper sequence: GLYMA18G01280.1 (Glycine max), 3'ss of exon 5
lower sequence: Vv17s0000g01840.t01 (Vitis vinifera), 3'ss of exon 5
gtaagttggaaagctcctgtggttgagctaacctctctccctctccccctctttttctctaggcattctcaaataatcatattatgatttcagGAATAACAAGAGATGGTTTATTAATGAGAATGAAGAAATCTCAATGGCAGGATGTTATTGATCTAAATCTCACTGGTGTTTTTCTTTGCACACAG
|| ||    |    |    || || |    |  | ||||  | |||       ||||  ||   ||| || |||           | ||| |||||| ||| | ||||| ||  | ||||||||||| ||| | ||||||||||| ||||||||| | |||||||| ||||| ||||| |||||||||
gttagcaacaggtatatcttgattcattgcaattatctcgatttcc-------tttcattaactattttccaat-----------ggttttagGAATTACACGGGATGGCTTGATGATGAGAATGAAAAAACCCCAATGGCAGGAGGTTATTGATTTGAATCTCACAGGTGTATTTCTCTGCACACAG

upper sequence: GLYMA18G01280.1 (Glycine max), 3'ss of exon 5
lower sequence: PP1S33_206V6.1 (Physcomitrella patens), 3'ss of exon 5
--------gtaagttggaaagctcctgtggttgagc--taacctctctccctctccccctctttttctctaggcattctcaaataatcatattatgatttcagGAATAACAAGAGATGGTTTATTAATGAGAATGAAGAAATCTCAATGGCAGGATGTTATTGATCTAAATCTCACTGGTGTTTTTCTTTGCACACAG
        |   || |      |   ||||| | |   |    |  |   || |     |  |||  |||       ||    |  |  |  |   | || |||||| || |  ||   ||| || ||||||||||||||    |||||||| ||||| || ||||| || ||||| |||||||||||||||||||||
ttgactatgcgtgtagtggtcgtgtagtggtcgtgtagtggggtaccaatctttgaggttgatttcgtcttaatggcct---gtgttgttggtgcaagtttagGAATTACGAAGGACACTTTGTTGATGAGAATGAAGAAGGAACAATGGCAAGATGTCATCGATCTCAACCTCACCGGTGTTTTTCTTTGCACACAG

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|58017082|gb|CX703824.1|CX703824
EST:     GCAGTTGATGCTTGGGGAACAGTTGATGTATTAATAAACAATGCAG                         GAATAACAAGAGATGGTTTATTAATGAGAATGAAGAAATCTCAATGGCAGG
genomic: GCAGTTGATGCTTGGGGAACAGTTGATGTATTAATAAACAATGCAGgtaagttgga ... atgatttcagGAATAACAAGAGATGGTTTATTAATGAGAATGAAGAAATCTCAATGGCAGG
EST: gi|213600146|gb|DB964310.1|DB964310
EST:     GCAGTTGATGCTTGGGGAACAGTTGATGTATTAATAAACAATGCAG                         GAATAACGAGAGATGGTTTATTAATGAGAATGAAGAAATCTCAATGGCAGG
genomic: GCAGTTGATGCTTGGGGAACAGTTGATGTATTAATAAACAATGCAGgtaagttgga ... atgatttcagGAATAACAAGAGATGGTTTATTAATGAGAATGAAGAAATCTCAATGGCAGG
EST: gi|7042369|gb|AW472263.1|AW472263
EST:     GCAGGTGATGCTTGGGGAACAGTTGATGTATTAATAAACAATGCAA                         GAATGACAAGAGATGGTTTA
genomic: GCAGTTGATGCTTGGGGAACAGTTGATGTATTAATAAACAATGCAGgtaagttgga ... atgatttcagGAATAACAAGAGATGGTTTA
EST: gi|192334676|gb|FK025223.1|FK025223
EST:     GCAGTTGATGCTTGGGGAACAGTTGATGTATTAATAAACAATGCAC                         GAATAACAAGAGATGGTTTATTAATGAGAATGAAGAAATCTCAATGGCAG-
genomic: GCAGTTGATGCTTGGGGAACAGTTGATGTATTAATAAACAATGCAGgtaagttgga ... atgatttcagGAATAACAAGAGATGGTTTATTAATGAGAATGAAGAAATCTCAATGGCAGG
EST: gi|192296853|gb|FG990229.1|FG990229
EST:     GCAGTGGATGCTTGGGGAACAGTTGATGTATTAATAAACAATGCAG                         GAATAACAAGAGATGGTTTATTAATGAGAATGAAGAAATCTCAATGGCAGG
genomic: GCAGTTGATGCTTGGGGAACAGTTGATGTATTAATAAACAATGCAGgtaagttgga ... atgatttcagGAATAACAAGAGATGGTTTATTAATGAGAATGAAGAAATCTCAATGGCAGG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ccctctccccctctttttctctaggcattctcaaataatcatattatgatttcagGAATAACAAGAGATGGTTTATTAATGAGAATGAAGAAATCTCAATGGCAGGATGTTATTGATCTAAATCTCACTGGTGTTTTTCTTTGCACACAG
                              tcaaataatcatatta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaagttggaaagctcctgtggttgagctaacctctctccctctccccctctttttctctaggcattctcaaataatcatattatgatttcagGAATAACAAGAGATGGTTTATTAATGAGAATGAAGAAATCTCAATGGCAGGATGTTATTGATCTAAATCTCACTGGTGTTTTTCTTTGCACACAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGGATG