RetrogeneDB ID: retro_mputfur_1446

Retrocopy location

• Organism: Ferret (Mustela putorius furo)
• Coordinates: GL897139.1:2216709..2217554(+)
• Located in intron of: ENSMPUG00000004438

Retrocopy information

• Ensembl ID: ENSMPUG00000004449
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: LDHA
• Ensembl ID: ENSMPUG00000013730
• Aliases: None
• Description: L-lactate dehydrogenase [Source:UniProtKB/TrEMBL;Acc:C6L2F2]

Sequence

>retro_mputfur_1446
GCCATCAGTATCTTAATGAAGGACTTGGCAGATGAACTTGCTCTTGTTGATGGCATGGAAGACAAATTCAATGGAGAGAT
GATGGATCTCCAGCATGGAAGCCTTTTCCTTAGAACACCAAAAATTGTCTCTGGCAAAGACTATAACGTGACTGCAAACT
CCAAGCTGGTTATTATCACAGCTGGGGCATGTCAGCAAGAGGGGGAAAGCCACCTTAATTTGGTCCAGCGTAACATGAAC
ATCTTTAAGTTCATCATTCCTAATGTCGTCAAATACAGCCAAACTGCAAGTTGCTTGTTGTTTCCAATCCAGTGAATATC
TTGACCTATGTGGCTTGGAAGATAAGTGGCTTTCCCAAAAACCGTGTTATTGGAAGTGGTTGCAATCTGGATTCAGCCCG
GTTCTGTTACCTAATGGGAGAAAGGCTGGGAGTTCACCCATTAAGCTGTCACGGGTGGATCCTCAGGGAGCATGGAGACT
CCAGTGTGCCTGTATGGAGTGGAGTAAACATTGCTGGTGTCTCTCTGAAGAATCTGCACCCTGACTTAGGCACTGATGCA
GATAAGGAACAGTGGAAAGAGGTTCACAAACAGGTGGTTAACAGTGCTTATGAGGTGATCAAACTGAAAGGCTTCACTTC
CTGGGCCATTGGACTGTCTGTGGCAGATTTGGCAGAAAGTATAATGAAGAATCTTAGGCAGGTGCATCCAATTTCCGCCA
TGATTAAGGGTCTCTATGGCATAAAAGATGATGTCTTCCTTAGTGTTCCTTGCATCTTGGGACAGAATGGAATTTCAGAT
GTTGTGAAGGTGACTCTGACTCCTGAGGAAGAGGCCCGTTTGAAG

Alignment

ORF - retro_mputfur_1446 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 94.7 %
• Parental protein coverage: 73.25 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  AISILMKDLADELALVDVMEDKLKGEMMDLQHGSLFLRTPKIVSGKDYNVTANSKLVIITAGARQQEGES
          AISILMKDLADELALVD.MEDK..GEMMDLQHGSLFLRTPKIVSGKDYNVTANSKLVIITAGA.QQEGES
Retrocopy AISILMKDLADELALVDGMEDKFNGEMMDLQHGSLFLRTPKIVSGKDYNVTANSKLVIITAGACQQEGES

Parental  RLNLVQRNVNIFKFIIPNVVKYS-PNCKLLVVSNPVDILTYVAWKISGFPKNRVIGSGCNLDSARFRYLM
          .LNLVQRN.NIFKFIIPNVVKYS.PNCKLLVVSNPV.ILTYVAWKISGFPKNRVIGSGCNLDSARF.YLM
Retrocopy HLNLVQRNMNIFKFIIPNVVKYS<PNCKLLVVSNPVNILTYVAWKISGFPKNRVIGSGCNLDSARFCYLM

Parental  GERLGVHPLSCHGWILGEHGDSSVPVWSGVNIAGVSLKNLHPDLGTDADKEQWKEVHKQVVDSAYEVIKL
          GERLGVHPLSCHGWIL.EHGDSSVPVWSGVNIAGVSLKNLHPDLGTDADKEQWKEVHKQVV.SAYEVIKL
Retrocopy GERLGVHPLSCHGWILREHGDSSVPVWSGVNIAGVSLKNLHPDLGTDADKEQWKEVHKQVVNSAYEVIKL

Parental  KGYTSWAIGLSVADLAESIMKNLRRVHPISTMIKGLYGIKDDVFLSVPCILGQNGISDVVKVTLTTEEEA
          KG.TSWAIGLSVADLAESIMKNLR.VHPIS.MIKGLYGIKDDVFLSVPCILGQNGISDVVKVTLT.EEEA
Retrocopy KGFTSWAIGLSVADLAESIMKNLRQVHPISAMIKGLYGIKDDVFLSVPCILGQNGISDVVKVTLTPEEEA

Parental  RLK
          RLK
Retrocopy RLK

Legend:

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

Expression

RNA-Seq

Mustela putorius furo was not studied using RNA-Seq expression data.

ChIP-Seq

Mustela putorius furo was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_mputfur_1446 retrocopy.

TSS

Mustela putorius furo was not studied using FANTOM5 data.

Lab

retro_mputfur_1446 was not experimentally validated.

Homology

Retrocopy orthology:

Mustela putorius furo 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 6 parental genes, and 23 retrocopies.

Species	Parental gene accession	Retrocopies number
Dipodomys ordii	ENSDORG00000003524	2 retrocopies	retro_dord_439, retro_dord_449,
Myotis lucifugus	ENSMLUG00000016343	4 retrocopies	retro_mluc_1716, retro_mluc_2031, retro_mluc_2440, retro_mluc_365,
Mustela putorius furo	ENSMPUG00000000172	5 retrocopies	retro_mputfur_1300, retro_mputfur_1561, retro_mputfur_492, retro_mputfur_539, retro_mputfur_549,
Mustela putorius furo	ENSMPUG00000013730	5 retrocopies	retro_mputfur_1256, retro_mputfur_133, retro_mputfur_1446 , retro_mputfur_1476, retro_mputfur_1565,
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,