RetrogeneDB ID: retro_itri_648

Retrocopy location

• Organism: Squirrel (Ictidomys tridecemlineatus)
• Coordinates: JH393309.1:93783..94599(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: None
• Aliases: None
• Status: NOVEL

Parental gene information

• Parental gene symbol: LDHB
• Ensembl ID: ENSSTOG00000022058
• Aliases: None
• Description: lactate dehydrogenase B [Source:HGNC Symbol;Acc:6541]

Sequence

>retro_itri_648
ATGGCAACCCTCAAGGAAAAACTCACTGCACCAGTTGCAGAAGAAGAGGTGACAGTCCCAAACAATAAGATCACTGTACT
GGGTGTTGGTCAAGTTGGTATGGCGTGTGCTACCAGCATTCTGGGAAAGTCTCTGGCTGATGAACTTCCTCTGGTGGATG
TTTTGGAAGATAAGCTCAAATGAGAAATGATGGATCTGCAGTATGGAAGCTTGTTTCTTCAAACACCTAAAATTGTGGCA
GATAAAGATTACTCTGTGACTGCCAATTCTAAGATAGTGGTAGTAACTGCAGGAGTCCATCAGCAGGAGGGGGAGAGTCG
TCTCAATCTTGTGCAGAGAAATGTCAATGTCTTCAAATTCATTATTCCTTAAATTGTCAAGTACAGTCCCGATTGCATCA
TAATTGTGCTTTCCAACCCAGTGGACATTCTTACATATGTTACCTGGAAACTAAGTGGATTACCCAAGCACCGTGTGATT
GGAAGTGGGTGTAATCTGGATTCTGCTAGATTTTGCTATCTTATGGCTGAGAAACTTGGCATTCATCCCAGCAGCTGCCA
CAGATGGATTCTGGGAGAACATGGCAAATCAAGTGTGGCTGTGTGAAGTGGAGTGAATGTGGCTGGTGTTTTTCTCCAGG
AACTAAATCCAGAAATGGGAACAGACAATGATAGTTAAAACTAGAAGAAAGTGCATAAGATGGTTGTTGAAAGTGCCTAT
GAAGTCATCAAGAAAAAAGGATACACCAACTGGGCTCTTGGGCTGACCTTATTGAATCCATGTGTAAAATCTATCCAGAA
TTCACCCAGTATCAAC

Alignment

ORF - retro_itri_648 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 83.33 %
• Parental protein coverage: 81.66 %
• Number of stop codons detected: 5
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MATLKEKLIAPVAEEETTVPNNKITVVGVGQVGMACAISILGKSLADELALVDVLEDKLKGEMMDLQHGS
          MATLKEKL.APVAEEE.TVPNNKITV.GVGQVGMACA.SILGKSLADEL.LVDVLEDKLK.EMMDLQ.GS
Retrocopy MATLKEKLTAPVAEEEVTVPNNKITVLGVGQVGMACATSILGKSLADELPLVDVLEDKLK*EMMDLQYGS

Parental  LFLQTPKIVADKVTSVTVNNEMVVVTAGVRQQEGESRLNLVQRNVNVFKFIIPQIVKYSPDCIIIVVSNP
          LFLQTPKIVADK..SVT.N...VVVTAGV.QQEGESRLNLVQRNVNVFKFIIP.IVKYSPDCIIIV.SNP
Retrocopy LFLQTPKIVADKDYSVTANSKIVVVTAGVHQQEGESRLNLVQRNVNVFKFIIP*IVKYSPDCIIIVLSNP

Parental  EYSVDILTYVTWKLSGLPKHRVIGSGCNLDSARFRYLMAEKLGIHPSSCHGWILGEHGDSSVVAVWSGVN
          ...VDILTYVTWKLSGLPKHRVIGSGCNLDSARF.YLMAEKLGIHPSSCH.WILGEHG.SS.VAV.SGVN
Retrocopy ---VDILTYVTWKLSGLPKHRVIGSGCNLDSARFCYLMAEKLGIHPSSCHRWILGEHGKSS-VAV*SGVN

Parental  VAGVSLQELNPEMGTDSDSENWKEVHKMVVESAYEVIKLKGYTNWAIGLSVADLIESMFKNLSRIH
          VAGV.LQELNPEMGTD.DS.N.K.VHKMVVESAYEVIK.KGYTNWA.GL...........N...I.
Retrocopy VAGVFLQELNPEMGTDNDS*N*KKVHKMVVESAYEVIKKKGYTNWALGLTLLNPCVKSIQNSPSIN

Legend:

• *: Stop codon
• >: Forward frameshift by one nucleotide
• <: Reverse frameshift by one nucleotide

Expression

RNA-Seq

Ictidomys tridecemlineatus was not studied using RNA-Seq expression data.

ChIP-Seq

Ictidomys tridecemlineatus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_itri_648 retrocopy.

TSS

Ictidomys tridecemlineatus was not studied using FANTOM5 data.

Lab

retro_itri_648 was not experimentally validated.

Homology

Retrocopy orthology:

Ictidomys tridecemlineatus does not belong to any of the species groups (eutheria, teleost or neognath), studied for retrocopy-based homology. For more information about studied groups, please go to help section.

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Parental genes homology:

Parental genes homology involve 16 parental genes, and 40 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000016175	4 retrocopies	retro_amel_1316, retro_amel_814, retro_amel_882, retro_amel_977,
Bos taurus	ENSBTAG00000019603	4 retrocopies	retro_btau_1589, retro_btau_303, retro_btau_451, retro_btau_647,
Canis familiaris	ENSCAFG00000012195	9 retrocopies	retro_cfam_1068, retro_cfam_111, retro_cfam_1674, retro_cfam_17, retro_cfam_1700, retro_cfam_174, retro_cfam_1836, retro_cfam_701, retro_cfam_93,
Cavia porcellus	ENSCPOG00000007138	1 retrocopy	retro_cpor_762,
Echinops telfairi	ENSETEG00000019955	1 retrocopy	retro_etel_850,
Felis catus	ENSFCAG00000012639	1 retrocopy	retro_fcat_462,
Macropus eugenii	ENSMEUG00000004825	1 retrocopy	retro_meug_311,
Myotis lucifugus	ENSMLUG00000012155	1 retrocopy	retro_mluc_202,
Macaca mulatta	ENSMMUG00000002679	4 retrocopies	retro_mmul_212, retro_mmul_303, retro_mmul_308, retro_mmul_315,
Monodelphis domestica	ENSMODG00000017786	1 retrocopy	retro_mdom_1484,
Mustela putorius furo	ENSMPUG00000000172	5 retrocopies	retro_mputfur_1300, retro_mputfur_1561, retro_mputfur_492, retro_mputfur_539, retro_mputfur_549,
Oryctolagus cuniculus	ENSOCUG00000022015	1 retrocopy	retro_ocun_805,
Sorex araneus	ENSSARG00000002565	1 retrocopy	retro_sara_713,
Sus scrofa	ENSSSCG00000000576	1 retrocopy	retro_sscr_37,
Ictidomys tridecemlineatus	ENSSTOG00000000014	3 retrocopies	retro_itri_1396, retro_itri_1526, retro_itri_535,
Ictidomys tridecemlineatus	ENSSTOG00000022058	2 retrocopies	retro_itri_501, retro_itri_648 ,