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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...caatattttttggtgattggtgatttgttattcttatatctgtgtcatgaaatattttttatgccatgcagactttaccatatttttctatcacttgcagGTATTCTGTTCCGAATTTTGGGCTACTATACAGGGCAACCTTTACTCGGGGCCAAAGTTGTGGCTGCTTTGCTCATGTTTGCAACAGTGTCTGGTATTCT

Basic information

species Glycine max
transcript GLYMA07G00350.1
intron # 13
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA07G00350.1 (Glycine max), 3'ss of exon 13
lower sequence: LOC_Os02g33490.1 (Oryza sativa), 3'ss of exon 13
caatattttttggtgattggtgatttgttattcttatatctgtgtcatgaaatattttttatgccatgcagactttaccatatttttctatcacttgcagGTATTCTGTTCCGAATTTTGGGCTACTATACAGGGCAACCTTTACTCGGGGCCAAAGTTGTGGCTGCTTTGCTCATGTTTGCAACAGTGTCTGGTATTCT
   ||  || |   |||  | |  || ||    || | |   |  | |    || ||||| |    || | |   |     |       ||   ||||||||||| | ||||| || |||||  ||  ||| || |  ||| | || || ||||||||||| || ||| |||| ||||||||||| || |||||||||||
--gtaagttctatagatatgggggttattgcatttttgttc-tagcgttgggtacttttttttttttgaaaa---tggggaaaccaatcatggtttgcagGTATTATCTTCCGTATGTTGGGTCACGCTACTGGCCGGCCTCTTCTTGGAGCCAAAGTTGTAGCCGCTATGCTTATGTTTGCAACTGTTTCTGGTATTCT

upper sequence: GLYMA07G00350.1 (Glycine max), 3'ss of exon 13
lower sequence: AT1G78920.2 (Arabidopsis thaliana), 3'ss of exon 13
caatattttttggtgattggtgatttgttattcttatatctgtgtcatgaaatatttt--ttatgccatgcagactttacc---atatttttctatcacttgcagGTATTCTGTTCCGAATTTTGGGCTACTATACAGGGCAACCTTTACTCGGGGCCAAAGTTGTGGCTGCTTTGCTCATGTTTGCAACAGTGTCTGGTATTCT
     |   |  || ||     | | ||| |||||   |   |||  |||||  ||      |   |||   |||   |     |  | ||  | || ||| ||||| |  |||| ||||| ||||| ||||| ||||| |||||| | ||||| || |||||||| ||| || ||||||||||||||||||| | ||||||  |
----gtaagtcagtaat-atctactcgtttttctttacttactgtattgaaagtttgaaaccacaacattgtgaccaaaaacaaacctcttgttctctctttcagGTTTGGTGTTTCGAATCTTGGGTTACTACACAGGACAACCTCTGCTCGGAGCAAAAGTTGTAGCTTCTATGCTCATGTTTGCAACAGTTTGTGGTATCTT

upper sequence: GLYMA07G00350.1 (Glycine max), 3'ss of exon 13
lower sequence: Vv09s0054g00700.t01 (Vitis vinifera), 3'ss of exon 13
---caatattttttggtgattg-gtgat-ttgttattcttatatct-gtgtcatgaaatattttttatgccatgcagactttaccatatttttctatcacttgcagGTATTCTGTTCCGAATTTTGGGCTACTATACAGGGCAACCTTTACTCGGGGCCAAAGTTGTGGCTGCTTTGCTCATGTTTGCAACAGTGTCTGGTATTCT
   |   |   ||| ||||||| ||||| ||| |||| |  | ||| || || |    |  ||||   ||  |       | | | ||| ||| |||| ||||||||  |||||||||| |||||||| ||||| || || || ||| |||||||||| |||||||||||| |  || | ||||||||||||||  | ||||| ||
aaccttcaaccttttgtgattgagtgatcttgctattttcgtttcttgtttcgttcggttattttggggcttt------ctcatcttatgtttatatcccttgcagGCTTTCTGTTCCGGATTTTGGGATACTACACCGGACATCCTCTACTCGGGGCTAAAGTTGTGGCTTCAATGTTGATGTTTGCAACAGTTGCGGGTATACT

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|15286246|gb|BI470137.1|BI470137
EST:     GAGATGATAAAACCTGGTGCTTTGGGCA-TCATTTCACCTATTGTAGTTG                         GTATTCTGTTCCGAATTTTGGGCTACTATACAGGGCAA
genomic: GAGATGATAAAACCTGGTGCTTTGG-CAATCATTTCACCTATTGTAGTTGgtgggttaac ... tcacttgcagGTATTCTGTTCCGAATTTTGGGCTACTATACAGGGCAA
EST: gi|58016814|gb|CX703556.1|CX703556
EST:     AGAGATGATAAAACCTGGTGCTTTGGCAATCATTTCACCTATTGTAGTTG                         GTATTCTGTTCCGAATTTTGGGCTACTATACAGGGCAACCTTTACTCGGGG
genomic: AGAGATGATAAAACCTGGTGCTTTGGCAATCATTTCACCTATTGTAGTTGgtgggttaac ... tcacttgcagGTATTCTGTTCCGAATTTTGGGCTACTATACAGGGCAACCTTTACTCGGGG
EST: gi|192305808|gb|FG995736.1|FG995736
EST:     AGAGATGATAAAACCTGGTGCTTTGGCAATCATTTCACCTATTGTAGTTG                         GTATTCTGTTCCGAATTTTGGGCTACTATACAGGGCAACCTTTACTCGGGG
genomic: AGAGATGATAAAACCTGGTGCTTTGGCAATCATTTCACCTATTGTAGTTGgtgggttaac ... tcacttgcagGTATTCTGTTCCGAATTTTGGGCTACTATACAGGGCAACCTTTACTCGGGG
EST: gi|57575699|gb|CX548674.1|CX548674
EST:     AGAGATGATAAAACCTGGTGCTTTGGCAATCATTTCACCTATTGTAGTTG                         GTATTCTGTTCCGAATTTTGGGCTACTATACAGGGCAACCTTTACTCGGGG
genomic: AGAGATGATAAAACCTGGTGCTTTGGCAATCATTTCACCTATTGTAGTTGgtgggttaac ... tcacttgcagGTATTCTGTTCCGAATTTTGGGCTACTATACAGGGCAACCTTTACTCGGGG
EST: gi|58018271|gb|CX705013.1|CX705013
EST:     AGAGATGATAAAACCTGGTGCTTTGGCAATCATTTCACCTATTGTAGTTG                         GTATTCTGTTCCGAATTTTGGGCTACTATACAGGGCAACCTTTACTCGGGG
genomic: AGAGATGATAAAACCTGGTGCTTTGGCAATCATTTCACCTATTGTAGTTGgtgggttaac ... tcacttgcagGTATTCTGTTCCGAATTTTGGGCTACTATACAGGGCAACCTTTACTCGGGG
EST: gi|58015021|gb|CX701763.1|CX701763
EST:     AGAGATGATAAAACCTGGTGCTTTGGCAATCATTTCACCTATTGTAGTTG                         GTATTCTGTTCCGAATTTTGGGCTACTATACAGGGCAACCTTTACTCGGGG
genomic: AGAGATGATAAAACCTGGTGCTTTGGCAATCATTTCACCTATTGTAGTTGgtgggttaac ... tcacttgcagGTATTCTGTTCCGAATTTTGGGCTACTATACAGGGCAACCTTTACTCGGGG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

catgaaatattttttatgccatgcagactttaccatatttttctatcacttgcagGTATTCTGTTCCGAATTTTGGGCTACTATACAGGGCAACCTTTACTCGGGGCCAAAGTTGTGGCTGCTTTGCTCATGTTTGCAACAGTGTCTGGTATTCT
                                     tttttctatcactt  CT-rich tract
     aatattttttat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
caatattttttggtgattggtgatttgttattcttatatctgtgtcatgaaatattttttatgccatgcagactttaccatatttttctatcacttgcagGTATTCTGTTCCGAATTTTGGGCTACTATACAGGGCAACCTTTACTCGGGGCCAAAGTTGTGGCTGCTTTGCTCATGTTTGCAACAGTGTCTGGTATTCT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGCT
- - - - tttggtg
- - - - - - - - - - tgatttg
- - - - - - - - - - - - - - - - - - -atctgtg
- - - - - - - - - - - - - - - - - - - - - - -catgaaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ccatgca