Skip to another splice site:
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 5'  3'   		2  
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 5'  3'   		5  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gtttgttcatattcccatctaagttgttcagaggtggcaaagttttacatcatcattgctaattgttttcttttcctttccaaatttcttaaatctatagGCTATGGTGGTGATGTTTGGCCCATACAACCAGCTCCAAAGGACCATCCATGGCGCTACATGCCAAACCATGCCATGACTCCTCATATTTCTGGCACCAC

Basic information

species Glycine max
transcript GLYMA19G01200.1
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA19G01200.1 (Glycine max), 3'ss of exon 4
lower sequence: LOC_Os06g29180.1 (Oryza sativa), 3'ss of exon 4
gtttgttcatattcccatctaagttgttcaga-ggtggcaaagttttacatcatcattgctaattgttttcttttcctttccaaatt--tcttaaatctatagGCTATGGTGGTGATGTTTGGCCCATACAACCAGCTCCAAAGGACCATCCATGGCGCTACATGCCAAACCATGCCATGACTCCTCATATTTCTGGCACCAC
   ||| | ||||   |   || || |    | | || |  | |  ||  ||    ||| | | | ||| ||||  | |   ||  |  |  |   |    ||| |||||||||||||| |||  |   |||||||| |||||||| || |||||||| |||||||| || ||||||||||| |||||||| ||||| || ||
--gtgtcc-tattgaaaaaaaaattataagaatgatgccgtattaatatttctatcttgatcaatatttcctttagcatgaaaacctcattcttccttctcagGATATGGTGGTGATGTCTGGTTCCCCCAACCAGCACCAAAGGATCACCCATGGCGATACATGCCTAATCATGCCATGACCCCTCATATCTCTGGGACTAC

upper sequence: GLYMA19G01200.1 (Glycine max), 3'ss of exon 4
lower sequence: GRMZM2G147714_T01 (Zea mays), 3'ss of exon 5
gtttgttcatattcccatctaagttgttcagaggtggcaaagttttacatcatcattgctaattgttttcttttcctttccaaatttctt---aaatctatagGCTATGGTGGTGATGTTTGGCCCATACAACCAGCTCCAAAGGACCATCCATGGCGCTACATGCCAAACCATGCCATGACTCCTCATATTTCTGGCACCAC
   ||   | |||   |||| |    |   ||  |        | ||   |  |||||     |  ||| | |  | |     || || |    | |    ||| |||||||||||||| |||  |  ||| ||||| |||||||| || || |||||||||||||| |||||||||||||| ||||| || ||||| || ||
--ctgcctacatttt-atctgaagaatagggaaataatgcgactatattcctacattgaccggtactttgtgtaacatggagcatctcattcccatttctcagGATATGGTGGTGATGTGTGGTTCCCACAGCCAGCACCAAAGGATCACCCCTGGCGCTACATGCCTAACCATGCCATGACCCCTCACATCTCTGGGACTAC

upper sequence: GLYMA19G01200.1 (Glycine max), 3'ss of exon 4
lower sequence: GRMZM2G418005_T01 (Zea mays), 3'ss of exon 3
gtttgttcatattcccatctaagttgttcagaggtggcaaagttttacatcatcattgctaattgttttcttttcctttccaaatttctt---aaatctatagGCTATGGTGGTGATGTTTGGCCCATACAACCAGCTCCAAAGGACCATCCATGGCGCTACATGCCAAACCATGCCATGACTCCTCATATTTCTGGCACCAC
   ||   | |||   |||| |    |   ||  |        | ||   |  |||||     |  ||| | |  | |     || || |    | |    ||| |||||||||||||| |||  |  ||| ||||| |||||||| || || |||||||||||||| |||||||||||||| ||||| || ||| | || ||
--ctgcctacatttt-atctgaagaatagggaaataatgcgactatattcctacattgaccggtactttgtgtaacatggagcatctcattcccatttctcagGATATGGTGGTGATGTGTGGTTCCCACAGCCAGCACCAAAGGATCACCCCTGGCGCTACATGCCTAACCATGCCATGACCCCTCACATCTCTAGGACTAC

upper sequence: GLYMA19G01200.1 (Glycine max), 3'ss of exon 4
lower sequence: GRMZM2G049811_T01 (Zea mays), 3'ss of exon 4
gtttgttcatattcccatctaagttgttcagaggtggcaaagttttacatcatcattgctaattgttttcttttcctttccaaatttctt---aaatctatagGCTATGGTGGTGATGTTTGGCCCATACAACCAGCTCCAAAGGACCATCCATGGCGCTACATGCCAAACCATGCCATGACTCCTCATATTTCTGGCACCAC
   ||   | |||   |||| |    |   ||  |        | ||   |  |||||     |  ||| | |  | |     || || |    | |    ||| || ||||||||||| |||  |  ||| ||||| |||||||| || || |||||||||||||| |||||||||||||| ||||| || ||||| || ||
--ctgcctacatttt-atctgaagaatagggaaataatgcgactatattcctacattgaccggtactttgtgtaacatggagcatctcattcccatttcccagGATACGGTGGTGATGTGTGGTTCCCACAGCCAGCACCAAAGGATCACCCCTGGCGCTACATGCCTAACCATGCCATGACCCCTCACATCTCTGGGACTAC

upper sequence: GLYMA19G01200.1 (Glycine max), 3'ss of exon 4
lower sequence: GRMZM2G362021_T01 (Zea mays), 3'ss of exon 6
--gtttgttcatattcccatctaagttgttcagaggtggcaaagttttacatcatcattgctaattgttttcttttcctttccaaatttcttaaatctatagGCTATGGTGGTGATGTTTGGCCCATACAACCAGCTCCAAAGGACCATCCATGGCGCTACATGCCAAACCATGCCATGACTCCTCATATTTCTGGCACCAC-------------
    | ||| ||||| | | |   | |   | ||  ||    |||| |   | ||  |||  ||||    | |   ||| | ||     |      || ||||| |         | |  ||  |  | | ||||| |||||||| || || |||||||||||||| |||||||||||||| ||||| || ||||| || ||             
ggactcgtttatatttctaac---gctaacccgacttgt---agttgtgt-ttatatttgtaaatttcagtttcgccctattcacccccc------ctctaggcgac--------tatcagGTTCCCATAGCCAGCACCAAAGGATCACCCCTGGCGCTACATGCCTAACCATGCCATGACCCCTCACATATCTGGGACTACAATTGATGCGCAT

upper sequence: GLYMA19G01200.1 (Glycine max), 3'ss of exon 4
lower sequence: GRMZM2G423972_T02 (Zea mays), 3'ss of exon 3
gtttgttcatattcccatctaagttgttcagaggtggcaaagttttacatcatcattgctaattgttttcttttcctttccaaatttctt---aaatctatagGCTATGGTGGTGATGTTTGGCCCATACAACCAGCTCCAAAGGACCATCCATGGCGCTACATGCCAAACCATGCCATGACTCCTCATATTTCTGGCACCAC
   ||   | |||   |||| |    |   ||  |        | ||   |  |||||  |  |  ||| | |  | |     || || |    | |    ||| |||||||||||||| |||  |  ||| ||||| |||||||| || || |||||||||||||| |||||||||||| | ||||| || ||||| || ||
--ctgcctacatttt-atctgaagaatagggaaataatgcgactatattcctacattgacaggtactttgtgtaacatggagcatctcattcccatttctcagGATATGGTGGTGATGTGTGGTTCCCACAGCCAGCACCAAAGGATCACCCCTGGCGCTACATGCCTAACCATGCCATGGCCCCTCACATCTCTGGGACTAC

upper sequence: GLYMA19G01200.1 (Glycine max), 3'ss of exon 4
lower sequence: GRMZM2G170602_T01 (Zea mays), 3'ss of exon 4
-----------------------------------------------------------------gtttgttcatattccc----atctaagttgttcagagg------tggcaaagtttt-----acatcatcattgctaattgttttcttttcctttccaaatttcttaaatctatagGCTATGGTGGTGATGTTTGGCCCATACAACCAGCTCCAAAGGACCATCCATGGCGCTACATGCCAAACCATGCCATGACTCCTCATATTTCTGGCACCAC
                                                                 |      || |  |      |     || || ||||||      |||| |  | |      ||  |||  | || |      | | | ||         | |     ||    ||| || || || ||||| |||| |   || || || || |||||||| || |||||||||||||| ||| | |||||||| ||||| || || ||||||||
gtatgtactggctgctgctgtgtcctcctcattttcagcgggttagcatctgttagcaccatggcgccaaaacagaagcttgaagaggcgggtcgtgcagaggaagaagtggcgagatatagaaaaacgccatgctcgccagactcatacgtctcaaactgttgtatgcgtgatgatcagGATACGGCGGCGATGTGTGGCACCCTCAGCCTGCGCCCAAGGACCACCCGTGGCGCTACATGCCCAACAACGCCATGACCCCTCACATCTCCGGCACCAC

upper sequence: GLYMA19G01200.1 (Glycine max), 3'ss of exon 4
lower sequence: Vv14s0066g01320.t01 (Vitis vinifera), 3'ss of exon 4
-----gtttgttcatattcccatctaagttgttcagaggtgg----caaagttttacatcat-cattgctaattgttttcttttcctttccaaatttcttaaatctatagGCTATGGTGGTGATGTTTGGCCCATACAACCAGCTCCAAAGGACCATCCATGGCGCTACATGCCAAACCATGCCATGACTCCTCATATTTCTGGCACCAC
     ||||   ||  ||    | |      ||      ||     ||| ||||    | || || |  | |  |        | | ||  || |||||   || |  ||| ||  |||| |||||||||     ||| ||||| || ||||||||||||||||| |||||||||||||| || ||||| ||||||||||||||||||||
gtaatgtttcagcacttttgagtttcttggatttgagtatgttgttcaatgtttctttttatgcagttttgaaagccaatgacttcattttaattttct--gattttcagGTTACAGTGGGGATGTTTGGTATCCACAGCCAGCCCCCAAGGACCATCCATGGCGGTACATGCCAAACCAAGCTATGACCCCTCATATTTCTGGCACCAC

upper sequence: GLYMA19G01200.1 (Glycine max), 3'ss of exon 4
lower sequence: PP1S106_16V6.1 (Physcomitrella patens), 3'ss of exon 7
---------------------------------------------gtttgttcatattcccatctaagttgttcagaggtggcaaagttttacatcatcattgctaattgttttcttttccttt----ccaaatttcttaaatctatagGCTATGGTGGTGATGTTTGGCCCATACAACCAGCTCCAAAGGACCATCCATGGCGCTACATGCCAAACCATGCCATGACTCCTCATATTTCTGGCACCAC
                                             | |     | | ||| |     | |   |||       ||       ||  |      ||  ||| |   |    |  |    |    |  |  ||||    ||| ||||| || ||||| |||  |   || || ||   |||||||||||| ||||| |||||||| ||||| |||||||| || ||||| || ||||| ||
gtaactcgacaacttccgaaaacttccgctcatcccctgcatgtcgctaacctagaatcctaggcttgcttaccaggaacatgaacaccaatcacgaatggctctggttgctggatcgatcgctaagccgtggtaaccgaaattggcagGATATGGAGGAGATGTATGGAACGCTCAGCCGGCAGGAAAGGACCATCCTTGGCGTTACATGCCGAACCACGCCATGACCCCCCATATCTCCGGCACGAC

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|58017267|gb|CX704009.1|CX704009
EST:     TATGGACACCCAAGCAATTGCTGATGCTTGCTCTAGTGGCCACGTTGCAG                         GCTATGGTGGTGATGTTTGGCCCATACAACCAGCTCCAAAGGACCATCCAT
genomic: TATGGACACCCAAGCAATTGCTGATGCTTGCTCTAGTGGCCACGTTGCAGgtaattctaa ... aaatctatagGCTATGGTGGTGATGTTTGGCCCATACAACCAGCTCCAAAGGACCATCCAT
EST: gi|33389257|gb|CA852464.1|CA852464
EST:     TATGGACACCCAAGCAATTGCTGATGCTTGCTCTAGTGGCCACGTTGCAG                         GCTATGGTGGTGATGTTTGGCCCATACAACCNTCTCCAAAGGACCATCCAT
genomic: TATGGACACCCAAGCAATTGCTGATGCTTGCTCTAGTGGCCACGTTGCAGgtaattctaa ... aaatctatagGCTATGGTGGTGATGTTTGGCCCATACAACCAGCTCCAAAGGACCATCCAT
EST: gi|22521954|gb|BU080765.1|BU080765
EST:     TATGGACACCCAAGCAATTGCTGATGCTTGCTCTAGTGGCCACGTTGCAG                         GNCTATGGTGGTGATGTTTGGCCCATACAACCAGCTCCAAAGGACCATCCA
genomic: TATGGACACCCAAGCAATTGCTGATGCTTGCTCTAGTGGCCACGTTGCAGgtaattctaa ... aaatctatagG-CTATGGTGGTGATGTTTGGCCCATACAACCAGCTCCAAAGGACCATCCA
EST: gi|19934596|gb|BQ079626.1|BQ079626
EST:     TATGGACACCCAAGCAATTGCTGATGCTTGCTCTAGTGGCCACGTTGCAG                         GCTATGGTGGTGATGTTTGGCCCATACAACCAGCTCCAAAGGACCATCCAT
genomic: TATGGACACCCAAGCAATTGCTGATGCTTGCTCTAGTGGCCACGTTGCAGgtaattctaa ... aaatctatagGCTATGGTGGTGATGTTTGGCCCATACAACCAGCTCCAAAGGACCATCCAT
EST: gi|58024603|gb|CX711344.1|CX711344
EST:     TATGGACACCCAAGCAATTGCTGATGCTTGCTCTAGTGGCCACGTTGCAG                         GCTATGGTGGTGATGTTTGGCCCATACAACCAGCTCCAAAGGACCATCCAT
genomic: TATGGACACCCAAGCAATTGCTGATGCTTGCTCTAGTGGCCACGTTGCAGgtaattctaa ... aaatctatagGCTATGGTGGTGATGTTTGGCCCATACAACCAGCTCCAAAGGACCATCCAT
EST: gi|37996280|gb|CF807869.1|CF807869
EST:     TATGGACACCCAAGCAATTGCTGATGCTTGCTCTAGTGGCCACGTTGCAG                         GCTATGGTGGTGATGTTTGGCCCATACAACCAGCTCCAAAGGACCATCCAT
genomic: TATGGACACCCAAGCAATTGCTGATGCTTGCTCTAGTGGCCACGTTGCAGgtaattctaa ... aaatctatagGCTATGGTGGTGATGTTTGGCCCATACAACCAGCTCCAAAGGACCATCCAT
EST: gi|9259484|gb|BE347639.1|BE347639
EST:     CAATTGCTGATGCTTGCTCTAGTGGCCACGTTGCAG                         GCTATGGTGGTGATGTTTGGCCCATACAACCAGCTCCAAAGGACCATCCAT
genomic: CAATTGCTGATGCTTGCTCTAGTGGCCACGTTGCAGgtaattctaa ... aaatctatagGCTATGGTGGTGATGTTTGGCCCATACAACCAGCTCCAAAGGACCATCCAT
EST: gi|192327787|gb|FK022066.1|FK022066
EST:     TATGGACACCCAAGCAATTGCTGATGCTTGCTCTAGTGGCCACGTTGCAG                         GCTATGGTGGTGGTGTTTGGCCCATACAACCAGCTCCAAAGGACCATCCAT
genomic: TATGGACACCCAAGCAATTGCTGATGCTTGCTCTAGTGGCCACGTTGCAGgtaattctaa ... aaatctatagGCTATGGTGGTGATGTTTGGCCCATACAACCAGCTCCAAAGGACCATCCAT
EST: gi|254315424|gb|GR825233.1|GR825233
EST:     TATGGACACCCAAGCAATTGCTGATGCTTGCTCTAGTGGCCACGTTGCAG                         GCTATGGTGGTGATGTTTGGCCCATACAACCAGCTCCAAAGGACCATCCAT
genomic: TATGGACACCCAAGCAATTGCTGATGCTTGCTCTAGTGGCCACGTTGCAGgtaattctaa ... aaatctatagGCTATGGTGGTGATGTTTGGCCCATACAACCAGCTCCAAAGGACCATCCAT
EST: gi|57576050|gb|CX549021.1|CX549021
EST:     TATGGACACCCAAGCAATTGCTGATGCTTGCTCTAGTGGCCACGTTGCAG                         GCTATGGTGGTGATGTTTGGCCCATACAACCAGCTCCAAAGGACCATCCAT
genomic: TATGGACACCCAAGCAATTGCTGATGCTTGCTCTAGTGGCCACGTTGCAGgtaattctaa ... aaatctatagGCTATGGTGGTGATGTTTGGCCCATACAACCAGCTCCAAAGGACCATCCAT
EST: gi|4300722|gb|AI443088.1|AI443088
EST:     TATGGACACCCAAGCAATTGCTGATGCTTGCTCTAGTGGCCACGTTGCAG                         GCTATGGTGGTGATGTTTGGCCCATACAACCAGCTCCAAAGGACCATCCAT
genomic: TATGGACACCCAAGCAATTGCTGATGCTTGCTCTAGTGGCCACGTTGCAGgtaattctaa ... aaatctatagGCTATGGTGGTGATGTTTGGCCCATACAACCAGCTCCAAAGGACCATCCAT
EST: gi|254315423|gb|GR825232.1|GR825232
EST:     TATGGACACCCAAGCAATTGCTGATGCTTGCTCTAGTGGCCACGTTGCAG                         GCTATGGTGGTGATGTTTGGCCCATACAACCAGCTCCAAAGGACCATCCAT
genomic: TATGGACACCCAAGCAATTGCTGATGCTTGCTCTAGTGGCCACGTTGCAGgtaattctaa ... aaatctatagGCTATGGTGGTGATGTTTGGCCCATACAACCAGCTCCAAAGGACCATCCAT
EST: gi|6848238|gb|AW350528.1|AW350528
EST:     TATGGACACCCAAGCAATTGCTGATGCTTGCTCTAGTGGCCACGTTGCAG                         GCTATGGTGGTGATGTTTGGCCCATACAACCAGCTCCAAAGGACCATCCAT
genomic: TATGGACACCCAAGCAATTGCTGATGCTTGCTCTAGTGGCCACGTTGCAGgtaattctaa ... aaatctatagGCTATGGTGGTGATGTTTGGCCCATACAACCAGCTCCAAAGGACCATCCAT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tacatcatcattgctaattgttttcttttcctttccaaatttcttaaatctatagGCTATGGTGGTGATGTTTGGCCCATACAACCAGCTCCAAAGGACCATCCATGGCGCTACATGCCAAACCATGCCATGACTCCTCATATTTCTGGCACCAC
           tgctaat  putative branch site (score: 2)
                                       tttctta  putative PPT
                                    aaatttcttaaatcta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtttgttcatattcccatctaagttgttcagaggtggcaaagttttacatcatcattgctaattgttttcttttcctttccaaatttcttaaatctatagGCTATGGTGGTGATGTTTGGCCCATACAACCAGCTCCAAAGGACCATCCATGGCGCTACATGCCAAACCATGCCATGACTCCTCATATTTCTGGCACCAC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTCCTC
- - - - - - - ccatcta
- - - - - - - - - - - - - - - gaggtgg