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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgagaacatcaaatatccaactatctatgctccttgttgataccctacatcatataagaatgaatttgttaattaatgtttacaattttttatttcagGTTGCTGTTGTGACAGTGGCATTTCCTGCAACCCCACTGCTACTGGCTAGAGCACGCATATGCATATCTGCAGCTCATTCAAGGGAAGACCTTATCAAAG

Basic information

species Glycine max
transcript GLYMA02G07250.1
intron # 10
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA02G07250.1 (Glycine max), 3'ss of exon 10
lower sequence: LOC_Os11g31640.1 (Oryza sativa), 3'ss of exon 10
-------------------gtga--gaacatcaaatatccaactatcta-tgctccttgttgataccctacatcatataagaatgaatttgttaattaatgtttacaattttttatttcagGTTGCTGTTGTGACAGTGGCATTTCCTGCAACCCCACTGCTACTGGCTAGAGCACGCATATGCATATCTGCAGCTCATTCAAGGGAAGACCTTATCAAAG
                   |  |   | | ||| | ||   ||    || || |  |||    |    |          ||     |||        | || |       |   |||||||||||||||||| || |||||||| ||||| || || ||||| || || || || ||||| ||||| |||||  | ||  | ||||| ||||| || ||||
gttagtaatggtatagaatgctatttatcttcagaaatggtacagaataatggtttttgccagttttttgtcgttccctagcccctattaccgtgcgactgatgtggcactggcatttcagGTTGCTGTTGTCACTGTGGCATTCCCTGCCACACCTCTGCTCCTTGCAAGGGCGCGCATCTGCATTTCTGCTTCGCACACTAGGGAGGACCTGATAAAAG

upper sequence: GLYMA02G07250.1 (Glycine max), 3'ss of exon 10
lower sequence: GRMZM2G152888_T01 (Zea mays), 3'ss of exon 10
gtgagaacatcaaatatccaactatctatgctccttgttgataccctacatcatataagaatgaatttgttaattaatgtttacaat-tttttatttcagGTTGCTGTTGTGACAGTGGCATTTCCTGCAACCCCACTGCTACTGGCTAGAGCACGCATATGCATATCTGCAGCTCATTCAAGGGAAGACCTTATCAAAG
 | | | ||      ||  |           ||  | ||   ||||       |          || ||| |    |  | ||  ||  || | || |||||||||||||| || || || |||||||| || || || || || ||||| |||||||||||||| |||||  | ||| | ||||| ||||| || ||||
ctaatagcaatctgcatatagtccatatccatcactatttgcacccactggtttcgttcttcctatctgtcatggtacttataagatacttatcttccagGTTGCTGTTGTTACTGTTGCGTTTCCTGCGACACCTCTTCTTCTTGCTAGGGCACGCATATGCATTTCTGCTTCACATACTAGGGAGGACCTGATGAAAG

upper sequence: GLYMA02G07250.1 (Glycine max), 3'ss of exon 10
lower sequence: GRMZM2G357734_T03 (Zea mays), 3'ss of exon 15
-------------------------------------------------------------------------------------------------gtgagaacatcaaatatccaactatctatgc---tccttgttgataccctacatcatataagaatgaatttgttaattaatgtttacaattttt-tatttcagGTTGCTGTTGTGACAGTGGCATTTCCTGCAACCCCACTGCTACTGGCTAGAGCACGCATATGCATATCTGCAGCTCATTCAAGGGAAGACCTTATCAAAG
                                                                                                 |||  || | |||    |      || ||     ||  | ||   ||||       |          || ||| |    |  | ||  ||  || | |||||||||| |||||| || || || |||||||| || || || || || ||||| |||||||||||||| |||||  | ||| | ||||| ||||| || ||||
gttagtagtagagtttgtcaggatattctgaagatccaaatagcactatgcttttggtatactttttttttttaaaatactttgtttgagaattgtggtgctaatagcaatctgcatgtagtccatttccatcactatttgcacccactggttttgttcttcctatctgtcatggtacttataagatacttatctttcagGTTGTTGTTGTTACTGTTGCGTTTCCTGCGACACCTCTTCTTCTTGCTAGGGCACGCATATGCATTTCTGCTTCACATACTAGGGAGGACCTGATTAAAG

upper sequence: GLYMA02G07250.1 (Glycine max), 3'ss of exon 10
lower sequence: GRMZM2G067257_T01 (Zea mays), 3'ss of exon 11
gtgagaacatcaaatatccaactatctatgctccttgttgataccctacatcatataagaatgaatttgttaattaatgtttacaat-tttttatttcagGTTGCTGTTGTGACAGTGGCATTTCCTGCAACCCCACTGCTACTGGCTAGAGCACGCATATGCATATCTGCAGCTCATTCAAGGGAAGACCTTATCAAAG
 | | | ||  |   ||  |      |    ||  | ||   ||||       |          || ||| |    |  | ||  ||  || | |||||||||| |||||| || || || |||||||| || || || || || ||||| |||||||||||||| |||||  | ||| | ||||| ||||| || ||||
ctaatagcaatatgcatgtagtccatttccatcactatttgcacccactggttttgttcttcctatctgtcatggtacttataagatacttatctttcagGTTGTTGTTGTTACTGTTGCGTTTCCTGCGACACCTCTTCTTCTTGCTAGGGCACGCATATGCATTTCTGCTTCACATACTAGGGAGGACCTGATTAAAG

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|51343322|gb|CO984055.1|CO984055
EST:     ACAACCCGGCCAAAATCCCTGCCTTTTCAAGAGAGTGCCTCAAGCAGAAT                         GTTGCTGTTGTGACAGTGGCATTTCCTGCAACCCCACTGCTACTGGCTAGA
genomic: ACAACCCGGCCAAAATCCCTGCCTTTTCAAGAGAGTGCCTCAAGCAGAATgtgagaacat ... tttatttcagGTTGCTGTTGTGACAGTGGCATTTCCTGCAACCCCACTGCTACTGGCTAGA
EST: gi|298177450|gb|HO023583.1|HO023583
EST:     ACAACCCGGCCAAAATCCCTGCCTTTTCAAGAGAGTGCCTCAAGCAGAAT                         GTTGCTGTTGTGACAGTGGCATTTCCTGCAACCCCACTGCTACTGGCTAGA
genomic: ACAACCCGGCCAAAATCCCTGCCTTTTCAAGAGAGTGCCTCAAGCAGAATgtgagaacat ... tttatttcagGTTGCTGTTGTGACAGTGGCATTTCCTGCAACCCCACTGCTACTGGCTAGA
EST: gi|10255864|gb|BE823630.1|BE823630
EST:     ACAACNNGGCCAAAATCCCTGCCTTTTCAAGAGAGTGCCTCAAGCAGAAT                         GTTGCTGTTGTGACAGTGGCATTTCCTGCAACCCCACTGCTACTGGCTAGA
genomic: ACAACCCGGCCAAAATCCCTGCCTTTTCAAGAGAGTGCCTCAAGCAGAATgtgagaacat ... tttatttcagGTTGCTGTTGTGACAGTGGCATTTCCTGCAACCCCACTGCTACTGGCTAGA
EST: gi|21677293|gb|BQ629644.1|BQ629644
EST:     ACAACCCGGCCAAAATCCCTGCCTTTTCAAGAGAGTGCCTCAAGCAGAAT                         GTTGCTGTTGTGACAGTGGCATTTCCTGCAACCCCACTGCTACTGGCTAGA
genomic: ACAACCCGGCCAAAATCCCTGCCTTTTCAAGAGAGTGCCTCAAGCAGAATgtgagaacat ... tttatttcagGTTGCTGTTGTGACAGTGGCATTTCCTGCAACCCCACTGCTACTGGCTAGA
EST: gi|213587414|gb|DB955538.1|DB955538
EST:     ACAACCCGGCCAAAATCCCTGCCTTTTCAAGAGAGTGCCTCAAGCAGAAT                         GTTGCTGTTGTGACAGTGGCATTTCCTGCAACCCCACTGCTACTGGCTAGA
genomic: ACAACCCGGCCAAAATCCCTGCCTTTTCAAGAGAGTGCCTCAAGCAGAATgtgagaacat ... tttatttcagGTTGCTGTTGTGACAGTGGCATTTCCTGCAACCCCACTGCTACTGGCTAGA
EST: gi|6454129|gb|AW184877.1|AW184877
EST:     ACAACCCGGCCAAAATCCCTGCCTTTTCAAGAGAGTGCCTCAAGCAGAAT                         GTTGCTGTTGTGACAGTGGCATTTCCTGCAACCCCACTGCTACTGGCTAGA
genomic: ACAACCCGGCCAAAATCCCTGCCTTTTCAAGAGAGTGCCTCAAGCAGAATgtgagaacat ... tttatttcagGTTGCTGTTGTGACAGTGGCATTTCCTGCAACCCCACTGCTACTGGCTAGA
EST: gi|15812369|gb|BI784644.1|BI784644
EST:     ACAACCCGGCCAAAATCCCTGCCTTTTCAAGAGAGTGCCTCAAGCAGAAT                         GTTGCTGTTGTGACAGTGGCATTTCCTGCAACCCCACTGCTACTGGCTAGA
genomic: ACAACCCGGCCAAAATCCCTGCCTTTTCAAGAGAGTGCCTCAAGCAGAATgtgagaacat ... tttatttcagGTTGCTGTTGTGACAGTGGCATTTCCTGCAACCCCACTGCTACTGGCTAGA
EST: gi|15200443|gb|BI424352.1|BI424352
EST:     ACAACCCGGCCAAAATCCCTGCCTTTTCAAGAGAGTGCCTCAAGCAGAAT                         GTTGCTGTTGTGACAGTGGCATTTCCTGCAACCCCACTGCTACTGGCTAGA
genomic: ACAACCCGGCCAAAATCCCTGCCTTTTCAAGAGAGTGCCTCAAGCAGAATgtgagaacat ... tttatttcagGTTGCTGTTGTGACAGTGGCATTTCCTGCAACCCCACTGCTACTGGCTAGA
EST: gi|209713090|gb|BW653797.1|BW653797
EST:     ACAACCCGGCCAAAATCCCTGCCTTTTCAAGAGAGTGCCTCAAGCAGAAT                         GTTGCTGTTGTGACAGTGGCATTTCCTGCAACCCCACTGCTACTGGCTAGA
genomic: ACAACCCGGCCAAAATCCCTGCCTTTTCAAGAGAGTGCCTCAAGCAGAATgtgagaacat ... tttatttcagGTTGCTGTTGTGACAGTGGCATTTCCTGCAACCCCACTGCTACTGGCTAGA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cctacatcatataagaatgaatttgttaattaatgtttacaattttttatttcagGTTGCTGTTGTGACAGTGGCATTTCCTGCAACCCCACTGCTACTGGCTAGAGCACGCATATGCATATCTGCAGCTCATTCAAGGGAAGACCTTATCAAAG
                           aattaat  putative branch site (score: 3)
                                          ttttttatttc  putative PPT
        atataagaatgaattt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgagaacatcaaatatccaactatctatgctccttgttgataccctacatcatataagaatgaatttgttaattaatgtttacaattttttatttcagGTTGCTGTTGTGACAGTGGCATTTCCTGCAACCCCACTGCTACTGGCTAGAGCACGCATATGCATATCTGCAGCTCATTCAAGGGAAGACCTTATCAAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGCAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CAGCTC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAAGA