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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ttttatcccattcaatttgtttgcttatcttatcacttctttttggttcataaggtggtttgaactctggttgggtttctttacaacaatcttcttgcagAATTTCGATGATGTCTTGTTTCCTGAAGACCATGTAAGTAGAAGCTATAATGATACTTACTACATAGATCCTCAGACTGTTTTAAGGTGTCACACAAGTG

Basic information

species Glycine max
transcript GLYMA02G10060.1
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA02G10060.1 (Glycine max), 3'ss of exon 2
lower sequence: Vv11s0103g00120.t01 (Vitis vinifera), 3'ss of exon 2
ttttatcccattcaatttgtttgctt-atcttatcacttctttttggttcataaggtggtttgaactctggttgggtttctttac-----aacaatcttcttgcagAATTTCGATGATGTCTTGTTTCCTGAAGACCATGTAAGTAGAAGCTATAATGATACTTACTACATAGATCCTCAGACTGTTTTAAGGTGTCACACAAGTG
|||| ||| | || || | ||| | | | | || || || | | | || || | | | || | ||||||||||||||| |||||||| ||| ||||| || || | ||||| || || |||||||| |||||||| |||||||| ||||| || ||||||||||| ||||
----atcctatttatagcacatgagagatttggtcaatgtctgct--tccaaaattcttattcatatttctatgaattcttatgccagaaaatatacttcttgcagAATTTTGATGATGTTTTGGTTCCTCCTGATCACATCAGTAGGAGTTACAATGATACATACTACATTGATCCTCAAACTGTCTTGAGGTGTCACACCAGTG

upper sequence: GLYMA02G10060.1 (Glycine max), 3'ss of exon 2
lower sequence: Vv19s0027g01380.t01 (Vitis vinifera), 3'ss of exon 2
ttttatcccattcaatttgtttgcttatcttatcacttctttttggttcataaggtggtttgaactctggttgggtttctttacaacaat----cttcttgcagAATTTCGATGATGTCTTGTTTCCTGAAGACCATGTAAGTAGAAGCTATAATGATACTTACTACATAGATCCTCAGACTGTTTTAAGGTGTCACACAAGTG
||| ||| | | || | || | | | | | | | | | || | | | || ||| ||||||||||||||| |||||||||||| ||||| || || | ||||| || || |||||||| |||||||| || |||| ||||| || ||||| ||||| ||||
----atcttatttataaggcatgggagttttggtcaatgtctgcttccaaaattcttatccatatttctgtgaattcttatgccagaaattttacttcttgcagAATTTTGATGATGTCTTGGTTCCTCCTGATCACATCAGTAGGAGTTACAATGATACATACTACATTGACTCTCAAACTGTCTTGAGGTGCCACACTAGTG

upper sequence: GLYMA02G10060.1 (Glycine max), 3'ss of exon 2
lower sequence: Vv19s0027g01220.t01 (Vitis vinifera), 3'ss of exon 2
ttttatcccattcaatttgtttgcttatcttatcacttctttttggttcataaggtggtttgaactctggttgggtttctttacaacaat-----cttcttgcagAATTTCGATGATGTCTTGTTTCCTGAAGACCATGTAAGTAGAAGCTATAATGATACTTACTACATAGATCCTCAGACTGTTTTAAGGTGTCACACAAGTG
|||| ||| | | || | | ||| | | | | || | | | | | || || | | | | || ||||||||||||||| |||||||||||| ||||| || || || |||||||| || |||||||| |||||||| || | || ||||| || ||||| ||||| ||||
---gatcctatttataaggcatggaagtttggtcaatgtctgct--tccaagattcttatccatatttctatgaattcttatgccagaaagtctacttcttgcagAATTTTGATGATGTCTTGGTTCCTCCTGATCACGTCAGTAGAAGTTACAATGATACATACTACATTGACTCCCAAACTGTCTTGAGGTGCCACACTAGTG

upper sequence: GLYMA02G10060.1 (Glycine max), 3'ss of exon 2
lower sequence: Vv19s0027g01200.t01 (Vitis vinifera), 3'ss of exon 1
ttttatcccattcaatttgtttgcttatcttatcacttctttttggttcataaggtggtttgaactctggt-tgggtttctttacaacaat-----cttcttgcagAATTTCGATGATGTCTTGTTTCCTGAAGACCATGTAAGTAGAAGCTATAATGATACTTACTACATAGATCCTCAGACTGTTTTAAGGTGTCACACAAGTG
|||| ||| | | || | || | | || ||| || | | | | | | || || | | | | || ||||||||||||||| |||||||||||| ||||| || || | ||||| || || |||||||| |||||||| || |||| ||||| || ||||| ||||| || |
----atcctatttataaggcatgggagttttg--gtcaatgtctgcttccaaaattcttatccatatttctatgaattcttatgccagaaagtctacttcttgcagAATTTTGATGATGTCTTGGTTCCTCCTGATCACATCAGTAGGAGTTACAATGATACATACTACATTGACTCTCAAACTGTCTTGAGGTGCCACACTAGGG

upper sequence: GLYMA02G10060.1 (Glycine max), 3'ss of exon 2
lower sequence: Vv19s0027g01150.t01 (Vitis vinifera), 3'ss of exon 3
ttttatcccattcaatttgtttgcttatcttatcacttctttttggttcataaggtggtttgaactctggt-tgggtttctttacaacaat-----cttcttgcagAATTTCGATGATGTCTTGTTTCCTGAAGACCATGTAAGTAGAAGCTATAATGATACTTACTACATAGATCCTCAGACTGTTTTAAGGTGTCACACAAGTG
|||| ||| | | || | || || | | || ||| || | | | | | | || || | | | | || ||||||||||||||| |||||||||||| ||||| || || || ||||| || || |||||||| |||||||| || |||| ||||| || ||||| ||||| | ||
----atcctatttataaggcatgggagttttg--gtttatgtctgcttccaaaattcttatccatatttctatgaattcttatgccagaaagtctacttcttgcagAATTTTGATGATGTCTTGGTTCCTCTTGATCACGTCAGTAGGAGTTACAATGATACATACTACATCGACTCTCAAACTGTCTTGAGGTGCCACACTACTG

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|23059943|gb|BU578399.1|BU578399
EST:     ATAAGTTCAACAAGTTTGATGATCTTTGTCCTATTGTTTCAGTGAAGCAG                         AATTTCGATGATGTCTTGTTTCCTGAAG
genomic: ATAAGTTCAACAAGTTTGATGATCTTTGTCCTATTGTTTCAGTGAAGCAGgtatggaaaa ... cttcttgcagAATTTCGATGATGTCTTGTTTCCTGAAG
EST: gi|193588475|gb|FK538754.1|FK538754
EST:     ATAAGTTCAACAAGTTTGATGATCTTTGTCCTATTGTTTCAGTGAAGCAG                         AATTTCGATGATGTCTTGTTTCCTGAAGACCATGTAAGTAGAAGCTATAAT
genomic: ATAAGTTCAACAAGTTTGATGATCTTTGTCCTATTGTTTCAGTGAAGCAGgtatggaaaa ... cttcttgcagAATTTCGATGATGTCTTGTTTCCTGAAGACCATGTAAGTAGAAGCTATAAT
EST: gi|18040970|gb|BM309264.1|BM309264
EST:     ATAAGTTCAACAAGTTTGATGATCTTTGTCCTATTGTTTCAGTGAAGCAG                         AATTTCGATGATGTCTTGTTTCCTGAAGACCATGTAAGTAGA
genomic: ATAAGTTCAACAAGTTTGATGATCTTTGTCCTATTGTTTCAGTGAAGCAGgtatggaaaa ... cttcttgcagAATTTCGATGATGTCTTGTTTCCTGAAGACCATGTAAGTAGA
EST: gi|22522222|gb|BU081033.1|BU081033
EST:     ATAAGTTCAACAAGTTTGATGATCTTTGTCCTATTGTTTCAGTGAAGCAG                         AATTTCGATGATGTCTTGTTTCCTGAAGACCATGTAAGTAGAAGCTATAAT
genomic: ATAAGTTCAACAAGTTTGATGATCTTTGTCCTATTGTTTCAGTGAAGCAGgtatggaaaa ... cttcttgcagAATTTCGATGATGTCTTGTTTCCTGAAGACCATGTAAGTAGAAGCTATAAT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gttcataaggtggtttgaactctggttgggtttctttacaacaatcttcttgcagAATTTCGATGATGTCTTGTTTCCTGAAGACCATGTAAGTAGAAGCTATAATGATACTTACTACATAGATCCTCAGACTGTTTTAAGGTGTCACACAAGTG
                                            tcttcttgc  CT-rich tract
 tttcttta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ttttatcccattcaatttgtttgcttatcttatcacttctttttggttcataaggtggtttgaactctggttgggtttctttacaacaatcttcttgcagAATTTCGATGATGTCTTGTTTCCTGAAGACCATGTAAGTAGAAGCTATAATGATACTTACTACATAGATCCTCAGACTGTTTTAAGGTGTCACACAAGTG

- - - -ccattca
- - - - - - - - -tgtttgc
- - - - - - - - - - - - - - - - - - - - - - - - - - -ggtggtt
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ggttggg