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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gttggtatatatttgtatttatatatttttatgttcagaggtacaataatcatattcatggaaaatgttctttgatatttgactcagGTTATTTTAACACCTACTCATCTGGCCATTGTAATGGAATATGCATCTGGTGGAGAACTATTTGAGAAAATCTGCAATGCAGGGCGTTTTAATGAGGATG

Basic information

species Glycine max
transcript GLYMA01G39020.2
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA01G39020.2 (Glycine max), 3'ss of exon 2
lower sequence: LOC_Os03g55600.1 (Oryza sativa), 3'ss of exon 2
gttggtatatatttgtatt-tatatatttttatgttcagaggtacaataatcatattcatggaaaatgttctttgatatttgact-cagGTTATTTTAACACCTACTCATCTGGCCATTGTAATGGAATATGCATCTGGTGGAGAACTATTTGAGAAAATCTGCAATGCAGGGCGTTTTAATGAGGATG
||  ||    || |  ||       ||| |   |||||    | ||||| |      ||   | || ||||| |   || |  || |||||||||||||| || |||||||| || ||||| ||||||||||| |||||||| || || || |||| ||| || ||    |  || || | ||| ||||
gtaagtcaggatcttcatgacgctcattctctagttcaccatt-caatattttccagcaaaaataa-gttctctatcatgtatctacagGTTATTTTAACCCCAACTCATCTTGCTATTGTCATGGAATATGCCTCTGGTGGTGAGCTTTTCGAGAGAATTTGTAAGAATGTACGGTTCAGTGAAGATG

upper sequence: GLYMA01G39020.2 (Glycine max), 3'ss of exon 2
lower sequence: GRMZM2G138861_T01 (Zea mays), 3'ss of exon 3
gttggtatatatttgtatttatatatttttatgttcagaggtacaataatcatattcatggaaaatgttctttgatatttgactcagGTTATTTTAACACCTACTCATCTGGCCATTGTAATGGAATATGCATCTGGTGGAGAACTATTTGAGAAAATCTGCAATGCAGGGCGTTTTAATGAGGATG
       |   || | |||   ||  | ||     |     | | ||  | | |    |    | | ||||||| ||| |     |||||||||||||||| || ||||| || ||||| ||||||||||| ||||| || || || |||||||  || || ||    | ||| || | ||| ||||
------gtgagttgggattgtgatgctgtttctccccagaattccattgttaaacatttttttattcttctttg-tatgt---ctagGTTATTTTAACACCGACCCATCTTGCTATTGTCATGGAATATGCCTCTGGCGGTGAGCTTTTTGAGAGGATATGTAAGAACGTGCGATTCAGTGAAGATG

upper sequence: GLYMA01G39020.2 (Glycine max), 3'ss of exon 2
lower sequence: GRMZM2G171435_T01 (Zea mays), 3'ss of exon 2
gttggtatatatttgtatttatatatt-tttatgttcagaggtacaataatcatattcatggaaaatgttctttgatatttgactcagGTTATTTTAACACCTACTCATCTGGCCATTGTAATGGAATATGCATCTGGTGGAGAACTATTTGAGAAAATCTGCAATGCAGGGCGTTTTAATGAGGATG
       |   || | |||   ||  | ||| |   |     | || |  | | |  | |   |||| |  ||  |||| |     |||||||||||||||| || ||||| || ||||| ||||||||||| ||||| || || || ||||||| ||| || ||    | ||| || | ||| ||||
------gtgagttgggattgtgatgctgtttctcccccagaattcatttgttaaacacttttgaaatttctttgtatatct-----agGTTATTTTAACACCGACCCATCTTGCTATTGTCATGGAATATGCCTCTGGCGGTGAGCTTTTTGAGAGAATATGTAAGAACGTGCGATTCAGTGAAGATG

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|6071033|gb|AW100420.1|AW100420
EST:     TCATTGATCACAGGTCTCTAAGACATCCTAACATTATCAGGTTTAAGGAG                         GTTATTTTAACACCTACTCATCTGGCCATTGTAATGGAATATGCATCTGGT
genomic: TCATTAATCACAGGTCTCTAAGACATCCTAACATTATCAGGTTTAAGGAGgttggtatat ... tttgactcagGTTATTTTAACACCTACTCATCTGGCCATTGTAATGGAATATGCATCTGGT
EST: gi|19453479|gb|BM954889.1|BM954889
EST:     TCATTAATCACAGGTCTCTAAGACATCCTAACATTATCAGGTTTAAGGAG                         GTTATTTTAACACCTACTCATCTGGCCATTGTAATGGAATATGCATCTGGT
genomic: TCATTAATCACAGGTCTCTAAGACATCCTAACATTATCAGGTTTAAGGAGgttggtatat ... tttgactcagGTTATTTTAACACCTACTCATCTGGCCATTGTAATGGAATATGCATCTGGT
EST: gi|11412769|gb|BF424780.1|BF424780
EST:     TCATTAATCACAGGTCTCTAAGACATCCTAACATTATCAGGTTTAAGGAG                         GTTATTTTAACACCTACTCATCTGGCCATTGTAATGGAATATGCATCTGGT
genomic: TCATTAATCACAGGTCTCTAAGACATCCTAACATTATCAGGTTTAAGGAGgttggtatat ... tttgactcagGTTATTTTAACACCTACTCATCTGGCCATTGTAATGGAATATGCATCTGGT
EST: gi|14259499|gb|BG882407.1|BG882407
EST:     TCATTAATCACAGGTCTCTAAGACATCCTAACATTATCAGGTTTAAGGAG                         GTTATTTTAACACCTACTCATCTGGCCATTGTAATGGAATATGCATCTGGT
genomic: TCATTAATCACAGGTCTCTAAGACATCCTAACATTATCAGGTTTAAGGAGgttggtatat ... tttgactcagGTTATTTTAACACCTACTCATCTGGCCATTGTAATGGAATATGCATCTGGT
EST: gi|4291115|gb|AI441715.1|AI441715
EST:     CATTAATCACAGGTCTCTAAGACATCCTAACCTTATCAGGGTTAAAGGAG                         GTTATTT-AACCAC-TACTCATCTGGCCAT
genomic: CATTAATCACAGGTCTCTAAGACATCCTAACATTATCAGGTTTAA-GGAGgttggtatat ... tttgactcagGTTATTTTAAC-ACCTACTCATCTGGCCAT
EST: gi|27424851|gb|CA936371.1|CA936371
EST:     TCATTAATCACAGGTCTCTAAGACATCCTAACATTATCAGGTTTAAGGAG                         GTCATTTTAACACCTACTCATCTGGCCATTGTAATGGAATATGCATCTGGT
genomic: TCATTAATCACAGGTCTCTAAGACATCCTAACATTATCAGGTTTAAGGAGgttggtatat ... tttgactcagGTTATTTTAACACCTACTCATCTGGCCATTGTAATGGAATATGCATCTGGT
EST: gi|18040782|gb|BM309076.1|BM309076
EST:     TCATTAATCACAGGTCTCTAAGACATCCTAACATTATCAGGTTTAAGGAG                         GTTATTTTAACACCTACTCATCTGGCCATTGTAATGGAATATGCATCTGGT
genomic: TCATTAATCACAGGTCTCTAAGACATCCTAACATTATCAGGTTTAAGGAGgttggtatat ... tttgactcagGTTATTTTAACACCTACTCATCTGGCCATTGTAATGGAATATGCATCTGGT
EST: gi|4286595|gb|AI441069.1|AI441069
EST:     TCATTAATCACAGGTCTCTAAGACATCCTAACATTATCAGGTTTAAAGAG                         GT-ATTTTAACACCTACTCATCT
genomic: TCATTAATCACAGGTCTCTAAGACATCCTAACATTATCAGGTTTAAGGAGgttggtatat ... tttgactcagGTTATTTTAACACCTACTCATCT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gttcagaggtacaataatcatattcatggaaaatgttctttgatatttgactcagGTTATTTTAACACCTACTCATCTGGCCATTGTAATGGAATATGCATCTGGTGGAGAACTATTTGAGAAAATCTGCAATGCAGGGCGTTTTAATGAGGATG
                                            atttgac  putative branch site (score: 4)
         tacaataatcatatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gttggtatatatttgtatttatatatttttatgttcagaggtacaataatcatattcatggaaaatgttctttgatatttgactcagGTTATTTTAACACCTACTCATCTGGCCATTGTAATGGAATATGCATCTGGTGGAGAACTATTTGAGAAAATCTGCAATGCAGGGCGTTTTAATGAGGATG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGGATG