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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ataataatatatgttttaatatctggtaatttctttgttttcctgaagtgttcgatctcttgtttgtttctgtgtaagtttatttctttcctgtctgcagAGTACAAGGTGCACACATACAACAGAAATGGTCTTTGCGCGTTGGGATTTATGGATGATCATTACCCGATTCGGAGTGCGTTTTCTCTTCTCAACCAG

Basic information

species Glycine max
transcript GLYMA13G19950.1
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA13G19950.1 (Glycine max), 3'ss of exon 1
lower sequence: LOC_Os01g64650.1 (Oryza sativa), 3'ss of exon 1
ataataatatatgttttaatatctggtaatttctttgttttcctgaagtgttcgatctcttgtttgtttctgtgtaagtttatttctttcctgtctgcagAGTACAAGGTGCACACATACAACAGAAATGGTCTTTGCGCGTTGGGATTTATGGATGATCATTACCCGATTCGGAGTGCGTTTTCTCTTCTCAACCAG
|   |    |   | || || |  |||    |  |        |  ||| | |  |   |  |         |||||     ||    |  | | |||||| |||||||| ||| || ||||||| ||||||||||||||  | | ||||||||||||||| || ||  | || ||||| ||||||||||| ||  ||
aatctgcagtcgatgttcattttcggtctagtgatcaggagaattcagtttgctgttgttaatgaacggtcatgtaaacaagttgtcctgatatttgcagAATACAAGGTCCACTCACACAACAGGAATGGTCTTTGCGCAGTTGCATTTATGGATGATCACTATCCTGTACGAAGTGCATTTTCTCTTCTGAATAAG

upper sequence: GLYMA13G19950.1 (Glycine max), 3'ss of exon 1
lower sequence: GRMZM2G387076_T02 (Zea mays), 3'ss of exon 2
ataataatatatgttttaatatctggt----aatttctttgttttcctgaagtgttcgatctcttgtttgtttctgtgtaagtttatttctttcctgtctgcagAGTACAAGGTGCACACATACAACAGAAATGGTCTTTGCGCGTTGGGATTTATGGATGATCATTACCCGATTCGGAGTGCGTTTTCTCTTCTCAACCAG
|||| | |||   |     | | || |    |  |      |     |    |||||  |  |    | | |  |||| | ||  | |   ||    | | |||| |||||||| ||| |  |||| |||||||| ||||| ||| | | ||| |||||||||||||| ||| | |||||||| ||||||||||| || |||
ataacattatggctgaccctgtttgctttagagatatggaatacatttttgctgttcatttcc--actcgctgttgtg-acgtacaatgtcttttcattt-cagAATACAAGGTCCACTCCCACAATAGAAATGGGCTTTGTGCGGTTGCATTCATGGATGATCATTATCCGGTACGGAGTGCATTTTCTCTTCTGAATCAG

upper sequence: GLYMA13G19950.1 (Glycine max), 3'ss of exon 1
lower sequence: GRMZM2G178244_T01 (Zea mays), 3'ss of exon 1
ataataatatatgttttaatatctggtaatttctttgttttcctgaagtgttcgatctct-tgtttgttt-ctgtgtaagtttatt-tctttcctgtctgcagAGTACAAGGTGCACACATACAACAGAAATGGTCTTTGCGCGTTGGGATTTATGGATGATCATTACCCGATTCGGAGTGCGTTTTCTCTTCTCAACCAG
   |||| |||||  | |   | |  |  |||     |||     |  | || | | ||  | |  |  | |||| |     ||   ||| | |    | |||| || ||||| ||| |  ||||||||||||| ||||| ||| ||| ||||||||||||||| || ||  | || ||||| ||||||||||| || |||
--cataacatatggctgaccctgtt-tgctttggagatttggaatacatttttgttgtccatttccgcatgctgttttgacatacaatctcttcccatttcagAATATAAGGTTCACTCCCACAACAGAAATGGGCTTTGTGCGGTGGCATTTATGGATGATCACTATCCTGTACGAAGTGCATTTTCTCTTCTGAATCAG

upper sequence: GLYMA13G19950.1 (Glycine max), 3'ss of exon 1
lower sequence: AT5G58060.1 (Arabidopsis thaliana), 3'ss of exon 1
ataataatatatgttttaatatctggtaatttctttgttttcctgaagtgttcgatctcttgtttgtttctgt--gtaagtttatttctttcctgtctgcagAGTACAAGGTGCACACATACAACAGAAATGGTCTTTGCGCGTTGGGATTTATGGATGATCATTACCCGATTCGGAGTGCGTTTTCTCTTCTCAACCAG
|  ||       | |||||| ||| |  |||   |  | ||  |  |||  ||||  |   | |  ||   ||  ||   |||||||  ||  ||  |  |||||||||||| ||| | ||||| |||||||| ||||||||| |||| || ||||| |||||||||||  |||| ||||| || ||||||||||| |||
actatgccccg-gctttaatttcttgcgattctatcttattgttctagtcctcgaatttgggataattagggttcgtgtttttattttgtttttggtt-tagAGTACAAGGTTCACGCTTACAATAGAAATGGCCTTTGCGCGGTGGGTTTCATGGACGATCATTACCCTGTTCGAAGTGCTTTCTCTCTTCTCAATCAG

upper sequence: GLYMA13G19950.1 (Glycine max), 3'ss of exon 1
lower sequence: AT5G58060.2 (Arabidopsis thaliana), 3'ss of exon 2
ataataatatatgttttaatatctggtaatttctttgttttcctgaagtgttcgatctcttgtttgtttctgtgtaagtttatttctttcctgtctgcagAGTACAAGGTGCACACATACAACAGAAATGGTCTTTGCGCGTTGGGATTTATGGATGATCATTACCCGATTCGGAGTGCGTTTTCTCTTCTCAACCAG
                                  || |  ||||  | | |  |||      || |  |  ||||   |||||||  ||  ||  |  |||||||||||| ||| | ||||| |||||||| ||||||||| |||| || ||||| |||||||||||  |||| ||||| || ||||||||||| |||
---------------------------------gttctagtcctcgaatttgggata----attagggttcgtgt--ttttattttgtttttggtt-tagagtacaagGTTCACGCTTACAATAGAAATGGCCTTTGCGCGGTGGGTTTCATGGACGATCATTACCCTGTTCGAAGTGCTTTCTCTCTTCTCAATCAG

upper sequence: GLYMA13G19950.1 (Glycine max), 3'ss of exon 1
lower sequence: Vv11s0206g00130.t01 (Vitis vinifera), 3'ss of exon 1
ataataatatatgttttaatatctggtaatttctttgttttcctgaagtgttcgatctcttgtttgtttctg-tgtaagtttatttctttcctgtctgcagAGTACAAGGTGCACACATACAACAGAAATGGTCTTTGCGCGTTGGGATTTATGGATGATCATTACCCGATTCGGAGTGCGTTTTCTCTTCTCAACCAG
 |  |  |   |||   ||  |||  |   |  |||| | |  |   |||       | |  |||||   || || |  ||  ||  |  | | | |  ||| || || |||||  | |||||||||||||||||||| ||  |||| ||||||||||| || || ||  |||| || || |||||  | |||||||||
gttttgtttcctgtgg-aaagtcttttgtatgttttgatatgttattgtgaagatgttttcttttgtaaatgctgaatattctttggtggcttttatatagAATATAAAGTGCATTCTTACAACAGAAATGGTCTTTGTGCACTGGGTTTTATGGATGACCACTATCCTGTTCGAAGCGCATTTTCCTTGCTCAACCAG

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|298168422|gb|HO009352.1|HO009352
EST:     CGTCGCCCGTCGCACCCCTCAGGGCCAACGCCAATCCGTACAACACGAAG                         AGTACAAGGTGCACACATACAACAGAAATGGTCTTTGCGCGTTGGGATTTA
genomic: CGTCGCCCGTCGCACCCCTCAGGGCCAACGCCAATCCGTACAACACGAAGgttctttttc ... ctgtctgcagAGTACAAGGTGCACACATACAACAGAAATGGTCTTTGCGCGTTGGGATTTA
EST: gi|192306907|gb|FK002629.1|FK002629
EST:     CGTCGCCCGTCGCACCCCTCAGGGCCAACGCCAATCCGTACAACACGAAG                         AGTACAAGGTGCACACATACAACAGAAATGGTCTTTGCGCGTTGGGATTTA
genomic: CGTCGCCCGTCGCACCCCTCAGGGCCAACGCCAATCCGTACAACACGAAGgttctttttc ... ctgtctgcagAGTACAAGGTGCACACATACAACAGAAATGGTCTTTGCGCGTTGGGATTTA
EST: gi|192299559|gb|FG987720.1|FG987720
EST:     CGTCGCCCGTCGCACCCCTCAGGGCCAACGCCAATCCGTACAACACGAAG                         AGTACAAGGTGCACACATACAACAGAAATGGTCTTTGCGCGTTGGGATTTA
genomic: CGTCGCCCGTCGCACCCCTCAGGGCCAACGCCAATCCGTACAACACGAAGgttctttttc ... ctgtctgcagAGTACAAGGTGCACACATACAACAGAAATGGTCTTTGCGCGTTGGGATTTA
EST: gi|298186143|gb|HO036776.1|HO036776
EST:     CGTCGCCCGTCGCACCCCTCAGGGCCAACGCCAATCCGTACAACACGAAG                         AGTACAGGGTGCACACATACAACAGAAATGGTCTTTGCGCGTTGGGATTTA
genomic: CGTCGCCCGTCGCACCCCTCAGGGCCAACGCCAATCCGTACAACACGAAGgttctttttc ... ctgtctgcagAGTACAAGGTGCACACATACAACAGAAATGGTCTTTGCGCGTTGGGATTTA
EST: gi|151393215|gb|EV263090.1|EV263090
EST:     CGTCGCCCGTCGCACCCCTCAGGGCCAACGCCAATCCGTACAACACGAAG                         AGTACAAGGTGCACACATACAACAGAAATGGTCTTTGCGCGTTGGGATTTA
genomic: CGTCGCCCGTCGCACCCCTCAGGGCCAACGCCAATCCGTACAACACGAAGgttctttttc ... ctgtctgcagAGTACAAGGTGCACACATACAACAGAAATGGTCTTTGCGCGTTGGGATTTA
EST: gi|193481169|gb|FK444832.1|FK444832
EST:     CGTCGCCCGTCGCACCCCTCAGGGCCAACGCCAATCCGTACAACACGAAG                         AGTACAAGGTGCACACATACAACAGAA-TGGTCTT
genomic: CGTCGCCCGTCGCACCCCTCAGGGCCAACGCCAATCCGTACAACACGAAGgttctttttc ... ctgtctgcagAGTACAAGGTGCACACATACAACAGAAATGGTCTT
EST: gi|151407036|gb|EV275591.1|EV275591
EST:     CGTCGCCCGTCGCACCCCTCAGGGCCAACGCCAATCCGTACAACACGAAG                         AGTACAAGGTGCACACATACAACAGAAATGGTCTTTGCGCGTTGGGATTTA
genomic: CGTCGCCCGTCGCACCCCTCAGGGCCAACGCCAATCCGTACAACACGAAGgttctttttc ... ctgtctgcagAGTACAAGGTGCACACATACAACAGAAATGGTCTTTGCGCGTTGGGATTTA
EST: gi|298197444|gb|HO044923.1|HO044923
EST:     CGTCGCCCGTCGCACCCCTCAGGGCCAACGCCAATCCGTACAACACGAAG                         AGTACAAGGTGCACACATACAACAGAAATGGTCTTTGCGCGTTGGGATTTA
genomic: CGTCGCCCGTCGCACCCCTCAGGGCCAACGCCAATCCGTACAACACGAAGgttctttttc ... ctgtctgcagAGTACAAGGTGCACACATACAACAGAAATGGTCTTTGCGCGTTGGGATTTA
EST: gi|213611777|gb|DB964781.1|DB964781
EST:     CGTCGCCCGTCGCACCCCTCAGGGCCAACGCCAATCCGTACAACACGAAG                         AGTACAAGGTGCACACATACAACAGAAATGGTCTTTGCGCGTTGGGATTTA
genomic: CGTCGCCCGTCGCACCCCTCAGGGCCAACGCCAATCCGTACAACACGAAGgttctttttc ... ctgtctgcagAGTACAAGGTGCACACATACAACAGAAATGGTCTTTGCGCGTTGGGATTTA
EST: gi|192294833|gb|FG987522.1|FG987522
EST:     CGTCGCCCGTCGCACCCCTCAGGGCCAACGCCAATCCGTACAACACGAAG                         AGTACAAGGTGCACACATACAACAGAAATGGTCTTTGCGCGTTGGGATTTA
genomic: CGTCGCCCGTCGCACCCCTCAGGGCCAACGCCAATCCGTACAACACGAAGgttctttttc ... ctgtctgcagAGTACAAGGTGCACACATACAACAGAAATGGTCTTTGCGCGTTGGGATTTA
EST: gi|298179750|gb|HO024965.1|HO024965
EST:     CGTCGCCCGTCGCACCCCTCAGGGCCAACGCCAATCCGTACAACACGAAG                         AGTACAAGGTGCACACATACAACAGAAATGGTCTTTGCGCGTTGGGATTTA
genomic: CGTCGCCCGTCGCACCCCTCAGGGCCAACGCCAATCCGTACAACACGAAGgttctttttc ... ctgtctgcagAGTACAAGGTGCACACATACAACAGAAATGGTCTTTGCGCGTTGGGATTTA
EST: gi|213602294|gb|DB958554.1|DB958554
EST:     CGTCGCCCGTCGCACCCCTCAGGGCCAACGCCAATCCGTACAACACGAAG                         AGTACAAGGTGCACACATACAACAGAAATGGTCTTTGCGCGTTGGGATTTA
genomic: CGTCGCCCGTCGCACCCCTCAGGGCCAACGCCAATCCGTACAACACGAAGgttctttttc ... ctgtctgcagAGTACAAGGTGCACACATACAACAGAAATGGTCTTTGCGCGTTGGGATTTA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aagtgttcgatctcttgtttgtttctgtgtaagtttatttctttcctgtctgcagAGTACAAGGTGCACACATACAACAGAAATGGTCTTTGCGCGTTGGGATTTATGGATGATCATTACCCGATTCGGAGTGCGTTTTCTCTTCTCAACCAG
                                 tttatttctttcctgt  CT-rich tract
                             taagtttatttcttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ataataatatatgttttaatatctggtaatttctttgttttcctgaagtgttcgatctcttgtttgtttctgtgtaagtttatttctttcctgtctgcagAGTACAAGGTGCACACATACAACAGAAATGGTCTTTGCGCGTTGGGATTTATGGATGATCATTACCCGATTCGGAGTGCGTTTTCTCTTCTCAACCAG

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