RetrogeneDB ID: retro_cfam_1946

Retrocopy location

• Organism: Dog (Canis familiaris)
• Coordinates: 8:28350227..28351187(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSCAFG00000014689
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

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

Sequence

>retro_cfam_1946
ATTCCTTTTGGTTCTAAGTCCAAAATGGCAACTCTCAAGGATCAGCTGATTCAGAATCTTCTTAAGGAAGACAATATCTC
CCAGAATAAGATTACAGTCATTGGGGTTGGTGCTATTGGCATGACTTGTGCCATCAGTATCTTAATGAAGGACTTGGCAG
ATGAACTCGCTCTTGTTGATGTCATGGAAGACAAATTGAAGGAAGAGACGATGGATCTCCAGCACAGCAGCCTTTTCTTT
AGAACACCAAAAATTGTCTCTGGCAAAGACTATAATGTGACTGCAAACTCCAAGCTGGCTATTATCACGGCTGGGGCATG
TCAGCAAGAGGGAGAAAGTCGTCTTAATTTGATCCAGCGTAACCTGAACATCTTTAAGTTCATCATTCCTAATATTGTCA
AATACAGCCCAAACTGCAAGTTGCTTGTTGTTTCCAATCCAGTGAATATCTTTACCTATGTGGCTTGGAAGATAACTGGC
TTTCCCAAAAACTGCATTATTGGAAGTGATTGCAATCTGGATTCAGCCCGGTTCCGTTACCTAATAGGGGAAAGGTTGGG
AGTTCACCCATTAAGCTGTCATAGGTGGGTCCTTGGAGAGCATGGAGACTCCAGTGTGCCTGTATGGAGTGGAGCAAATG
TTGCTGGTGTCTCTCTGAAGAATCTGCACCCTGACTTAGGCACTGATGCAGATAAGGAACAGTGGAAAGAGGTTTACAAA
CAGGTGGTTGACAGTGCCTATGAGGTGATCAAACTGAAAGGCTACACTTCCTGGGCCATTGGACTGTCTGTGGCAGATTT
GGCAGAAAGTATAACGAAGAATTTTAGGTGGGTGCATCCAATTTCCACCATGATTAAGGGTCTCTATGGAATAAAAGATG
ATGTCTTCCTTAGTGTTCCTTGCATCTTGGGGCAGAATGGAATCTCCGATGTGAGAGTGACTCTGACTCCTGAGGAAGAG

Alignment

ORF - retro_cfam_1946 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 90.65 %
• Parental protein coverage: 88.92 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  IPFGSKSKMATLKDQLIQNLLKEDHTPQNKITVVGVGAVGMACAISILMKDLADELALVDVMEDKLKGEM
          IPFGSKSKMATLKDQLIQNLLKED...QNKITV.GVGA.GM.CAISILMKDLADELALVDVMEDKLK.E.
Retrocopy IPFGSKSKMATLKDQLIQNLLKEDNISQNKITVIGVGAIGMTCAISILMKDLADELALVDVMEDKLKEET

Parental  MDLQHGSLFLRTPKIVSGKDYNVTANSKLVIITAGARQQEGESRLNLVQRNVNIFKFIIPNIVKYSPNCK
          MDLQH.SLF.RTPKIVSGKDYNVTANSKL.IITAGA.QQEGESRLNL.QRN.NIFKFIIPNIVKYSPNCK
Retrocopy MDLQHSSLFFRTPKIVSGKDYNVTANSKLAIITAGACQQEGESRLNLIQRNLNIFKFIIPNIVKYSPNCK

Parental  LLVVSNPVDILTYVAWKISGFPKNRVIGSGCNLDSARFRYLMGERLGVHPLSCHGWVLGEHGDSSVPVWS
          LLVVSNPV.I.TYVAWKI.GFPKN..IGS.CNLDSARFRYL.GERLGVHPLSCH.WVLGEHGDSSVPVWS
Retrocopy LLVVSNPVNIFTYVAWKITGFPKNCIIGSDCNLDSARFRYLIGERLGVHPLSCHRWVLGEHGDSSVPVWS

Parental  GVNVAGVSLKNLHPDLGTDADKEQWKQVHKQVVDSAYEVIKLKGYTSWAIGLSVADLAESIMKNLRRVHP
          G.NVAGVSLKNLHPDLGTDADKEQWK.V.KQVVDSAYEVIKLKGYTSWAIGLSVADLAESI.KN.R.VHP
Retrocopy GANVAGVSLKNLHPDLGTDADKEQWKEVYKQVVDSAYEVIKLKGYTSWAIGLSVADLAESITKNFRWVHP

Parental  ISTMIKGLYGIKDDVFLSVPCILGQNGISDVVKVTLTPEEE
          ISTMIKGLYGIKDDVFLSVPCILGQNGISDV..VTLTPEEE
Retrocopy ISTMIKGLYGIKDDVFLSVPCILGQNGISDV-RVTLTPEEE

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	0.08 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_1946 retrocopy.

TSS

Canis familiaris was not studied using FANTOM5 data.

Lab

retro_cfam_1946 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cfam_1946 has 0 orthologous retrocopies within eutheria group .

---

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,