RetrogeneDB ID: retro_cfam_1317

Retrocopy location

• Organism: Dog (Canis familiaris)
• Coordinates: 29:32654601..32655598(-)
• Located in intron of: ENSCAFG00000031788

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_1317
TCCAAGATGGCAACTGTGAGGTGCAAACTGATTAAGAATTTCACTTCGAAGGAGACCATTCATCACAATACGATCTCTCT
TCTAGAAACTGAATCACTTGGCATAGCGTGTGCTATCAGTATCGTATTAAAAGGCTTGAGTGATGAACTTGCCTTTGTGG
ATGTTGATGAATGCAAACTGAAGGGTGAGACAAGGGATGTTCAACATGGAAGCTCTTTCATGAAAATGCCAGATACTGTT
TTCAACAAAGATGACCATGTCACTGCAAACCCCAGCCTAGTGATTATCACAGCAGGTGCACACTCAGGGAAAGGAGAGAC
ACATCTTGATGTAGTCCAGAGAAATGTGTCCATCTTTAAATTAACGATTTCCAACATTACCCAGTGTAGTCCTCAGTGCA
AAATGATAATTGTTCCAATCCAGTGGATATCTTAACTTATGTAACTTGGAAGTTGAATGCCTTTTCCAAAACCGTATTAT
TGGAAGTGACTGTAATCTGGACGCTACCCGTTTCCATTTCTTTGTTGGGCAGAGACTTATTAGTATCCACTCAGAAAGCT
GTCATGGTTGGGTCCTTGGAGAGCATAGAGACTCAAGTGTACCTGAGTGGAGTGGAGTGAACATTGCTGGTATCCCCTTG
AAGGATCTGAATTCAGATATATGAATGGATAAAGATCCTGAGCCCTGGGAAAATGTCCAGAAAGAAATGATAACCTGTGG
CTATGAGATGGTTAAAATGAAAGGGTATACTAATTGGGCTGGTGGCCTATCTATAGCTGATTTAACGGAAAGCATTTTGA
AGAATCTTAGGAGAATGCATCAAGTTTCCACTATAACTAAGGGCCTCTGTAGAATAAATGAAGTATTCCTTATTGTCCCT
TATATCCTGGGATAGAATGGTATTGCAAACCTTACTAAGATAAAGCTGACCCCTGAAGAGGAAGTCTATTTGAGAAAGAG
TGCAGAAAGACTTTGGGAAATTCAGGAAGAGATCAAG

Alignment

ORF - retro_cfam_1317 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 56.85 %
• Parental protein coverage: 92.24 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  SKMATLKDQLIQNLLKEDHTPQNKITVVGVGAVGMACAISILMKDLADELALVDVMEDKLKGEMMDLQHG
          SKMAT....LI.N.........N.I........G.ACAISI..K.L.DELA.VDV.E.KLKGE..D.QHG
Retrocopy SKMATVRCKLIKNFTSKETIHHNTISLLETESLGIACAISIVLKGLSDELAFVDVDECKLKGETRDVQHG

Parental  SLFLRTPKIVSGKDYNVTANSKLVIITAGARQQEGESRLNLVQRNVNIFKFIIPNIVKYSPNCKLLVV-S
          S.F...P..V..KD..VTAN..LVIITAGA....GE..L..VQRNV.IFK..I.NI...SP.CK...V.S
Retrocopy SSFMKMPDTVFNKDDHVTANPSLVIITAGAHSGKGETHLDVVQRNVSIFKLTISNITQCSPQCKMIIV<S

Parental  NPVDILTYVAWKISGFPK-NRVIGSGCNLDSARFRYLMGERL-GVHPLSCHGWVLGEHGDSSVPVWSGVN
          NPVDILTYV.WK...F.K.NR.IGS.CNLD..RF....G.RL...H..SCHGWVLGEH.DSSVP.WSGVN
Retrocopy NPVDILTYVTWKLNAFSK<NRIIGSDCNLDATRFHFFVGQRLISIHSESCHGWVLGEHRDSSVPEWSGVN

Parental  VAGVSLKNLHPDLGTDADKEQWKQVHKQVVDSAYEVIKLKGYTSWAIGLSVADLAESIMKNLRRVHPIST
          .AG..LK.L..D...D.D.E.W..V.K......YE..K.KGYT.WA.GLS.ADL.ESI.KNLRR.H..ST
Retrocopy IAGIPLKDLNSDI*MDKDPEPWENVQKEMITCGYEMVKMKGYTNWAGGLSIADLTESILKNLRRMHQVST

Parental  MIKGLYGIKDDVFLSVPCILGQNGISDVVKVTLTPEEEARLKKSADTLWGIQKELQ
          ..KGL..I...VFL.VP.ILG.NGI....K..LTPEEE..L.KSA..LW.IQ.E..
Retrocopy ITKGLCRI-NEVFLIVPYILG*NGIANLTKIKLTPEEEVYLRKSAERLWEIQEEIK

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	0.04 RPM	130.66 RPM
SRP017611_brain	0.08 RPM	167.60 RPM
SRP017611_kidney	0.07 RPM	598.03 RPM
SRP017611_liver	0.07 RPM	198.69 RPM

ChIP-Seq

Canis familiaris was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cfam_1317 retrocopy.

TSS

Canis familiaris was not studied using FANTOM5 data.

Lab

retro_cfam_1317 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cfam_1317 has 1 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Equus caballus	retro_ecab_1004

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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,