RetrogeneDB ID: retro_cfam_2006

Retrocopy location

• Organism: Dog (Canis familiaris)
• Coordinates: 9:43522122..43522807(-)
• Located in intron of: ENSCAFG00000018898

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSCAFG00000009211
• Aliases: None
• Description: L-lactate dehydrogenase [Source:UniProtKB/TrEMBL;Acc:E2RA64]

Sequence

>retro_cfam_2006
CCCCAGGATAAGATTACAGTTGTTAGGGTTGGTTCTGTTGGCATGGCCTATGGCATGACGAGTCTCTTAATGAAGGACTT
GGCAGATGAACTTGTTCTGGTTGATGTCATGGAAAACAAACTGAAGGGAGACATGATGGCTCTCCAAAATGGCAGCCTTC
TTATAACACCAAAAATTGTCTCTGTCTCTGTCTACTACAACATGACTGCAAGCTCCAAGCTGGTTATTTCATCACAGCTA
GGGACATGTCAGCAACAGAGAGAAAGCCATCTTAATTTGGTCCAGCATAAATGGAACATCTTTAAATCCATCATTCCTAA
TATTGTAAAATACAGCCTAAACTGCAAGTCACTTGTTTCCAATCCAGTGGATATCTTGACTTTCGTGGCTTGGAAAATAA
GCAGCTTTCCCAAAATACTATGTTATTGGAAGTAGTTGCAATCTGGATTGAGTCCAGTTCTGTTACTTAATGGGGGAAAA
GCTGTGAGTTCACCCATTAAACTGTCATGAGTGGGTACTTGGGGAGCACGGAGAATCAGTGTACCTGTATGGAGTAAATG
TTGCTAGTGTCTCCCAGAAAAATCTGTGCCTGGACTTTGGCACTAATACAGATAAGGAACAGTGGCAAGAGGTTCACAAA
CAGGTGATTGACAGTGCCTGTGAGATGATCAAACTGAAAGACTAC

Alignment

ORF - retro_cfam_2006 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 69.53 %
• Parental protein coverage: 63.43 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  PQNKITVVGVGAVGMACAI-SILMKDLADELALVDVMEDKLKGEMMDLQHGSLFLRTPKIVS-GKDYNVT
          PQ.KITVV.VG.VGMA....S.LMKDLADEL.LVDVME.KLKG.MM.LQ.GSL...TPKIVS....YN.T
Retrocopy PQDKITVVRVGSVGMAYGMTSLLMKDLADELVLVDVMENKLKGDMMALQNGSLLI-TPKIVSVSVYYNMT

Parental  ANSKLVIITA-GARQQEGESRLNLVQRNVNIFKFIIPNIVKYSPNCKLLVVSNPVDILTYVAWKISGFPK
          A.SKLVI....G..QQ..ES.LNLVQ...NIFK.IIPNIVKYS.NCK.LV.SNPVDILT.VAWKIS.FPK
Retrocopy ASSKLVISSQLGTCQQQRESHLNLVQHKWNIFKSIIPNIVKYSLNCKSLV-SNPVDILTFVAWKISSFPK

Parental  -NRVIGSGCNLDSARFRYLMGERLGVHPLSCHGWVLGEHGDSSVPVWSGVNVAGVSLKNLHPDLGTDADK
          ...VIGS.CNLD...F.YLMGE.L.VHPL.CH.WVLGEHG..SV....GVNVA.VS.KNL..D.GT..DK
Retrocopy >YYVIGSSCNLD*VQFCYLMGEKL*VHPLNCHEWVLGEHGE-SVYLY-GVNVASVSQKNLCLDFGTNTDK

Parental  EQWKQVHKQVVDSAYEVIKLKGY
          EQW..VHKQV.DSA.E.IKLK.Y
Retrocopy EQWQEVHKQVIDSACEMIKLKDY

Legend:

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

Expression

RNA-Seq

Expression validation based on RNA-Seq data:

Library	Retrocopy expression	Parental gene expression
SRP012049_cerebellum	0.00 RPM	130.66 RPM
SRP017611_brain	0.00 RPM	167.60 RPM
SRP017611_kidney	0.00 RPM	598.03 RPM
SRP017611_liver	0.00 RPM	198.69 RPM

ChIP-Seq

Canis familiaris was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cfam_2006 retrocopy.

TSS

Canis familiaris was not studied using FANTOM5 data.

Lab

retro_cfam_2006 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cfam_2006 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 7 parental genes, and 34 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000009211	8 retrocopies	retro_cfam_1061, retro_cfam_1149, retro_cfam_1182, retro_cfam_1317, retro_cfam_1617, retro_cfam_1946, retro_cfam_2006 , retro_cfam_309,
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,
Dipodomys ordii	ENSDORG00000003524	2 retrocopies	retro_dord_439, retro_dord_449,
Felis catus	ENSFCAG00000015735	4 retrocopies	retro_fcat_102, retro_fcat_1839, retro_fcat_1919, retro_fcat_295,
Myotis lucifugus	ENSMLUG00000016343	4 retrocopies	retro_mluc_1716, retro_mluc_2031, retro_mluc_2440, retro_mluc_365,
Ictidomys tridecemlineatus	ENSSTOG00000000014	3 retrocopies	retro_itri_1396, retro_itri_1526, retro_itri_535,
Tarsius syrichta	ENSTSYG00000008062	4 retrocopies	retro_tsyr_1811, retro_tsyr_2064, retro_tsyr_2071, retro_tsyr_731,