RetrogeneDB ID: retro_cpor_685

Retrocopy location

• Organism: Guinea Pig (Cavia porcellus)
• Coordinates: scaffold_23:22158187..22159715(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSCPOG00000025021
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: DLD
• Ensembl ID: ENSCPOG00000005312
• Aliases: None
• Description: Dihydrolipoyl dehydrogenase [Source:UniProtKB/TrEMBL;Acc:H0V559]

Sequence

>retro_cpor_685
ATGCAGAGCTGGAATCGTGTGTACCGCTCCTTGGCCAAGAGAGGGCATTTCAATCAGATATCTCATGGCCTGCAGGGAGT
TTCTGCAGTACCTCTGAGAACTTATGCAGATCAATCGATTGATGCCGATGTAAAGGTGATAGGTTCTGGTCCTGGCGGTT
ATGGGTATGTTGCTGCCATTAAAGCTGCGCAGTTAGGCTTTAAGACAGTCTGCGTTGAGAAAAATGAAATACTTGGTGGA
ACATGCTTGAACGTTGGTTGTATTCCTTCTAAGGCTTTATTGAATAACTCTCATTACTATCATATGGCCCATGGAAAAGA
CTTTGCTTCTAGGGGAATTGAAATGTCTGAAGTTCGCTTGAATTTAGAGAAGATGATGGAGCAGAAGACGAATGCAGTAA
AAGCTTTAACAGGAGGAATTGCCCATTTATTCAAACAAAATAAGGTAGTTCACGTCAATGGGTTCGGAAAGATAACAGGC
AAAAACCAGGTCACAGCTACAAAAGCTGATGGCAGCACTCAGGATATTGATACAAAGAACATCCTAATAGCTACCGGTTC
AGAAATCACTCCTTTTCCTGGAATCACGATTGATGAAGATACAATAGTGTCATCTACAGGTGCTTTATCTTTAAAAAAAG
TTCCAGAAAAGATGTTTGTCATCGGTGCAGGTGTAATTGGCGTAGAATTGGGCTCCATCTGGCAAAGACTTGGTGCCGAT
GTGACAGCAGTTGAGTTTCTGGGTCACGTAGGTGGAGTCGGAATCGACATGGAGATATCTAAGAATTTTCAGCGGATCCT
TCAAAAGCAAGGGTTTAAATTTAAATTGAACACAAATGTTACTGGGGCCACCAAGAAGTCAGATGGAAAAATCGATGTTT
CCATTGAAGCTGCTTCTGGTGGGAAAGCTGAAGTCATCACGTGTGATGTACTCTTGGTTTGCATTAGTCCCTATTACTCA
GAATTTGGGACTAGAAGAACTTGGAATTGAACTGGATCCCAGAAGCAGAATTCCAGTCAATAGCAGATTCCAAACTAAAG
TTCCAAACATCTATGCCATCGGGGAAGTGGTGGCCGGCCCAATGCTGGCTCACAAGGCAGAGGATGAAGGCATCATCTGC
GTGGAAGGCATGGCTGGCGGCGCGGTGCACATGGACTACAGCTGTGTGCCATCGGTGATCTACACGCACCCTGAGGTGGC
CTGGGTCGGCAAATCGGAAGAGCAGTTGAAGGAGGAGGGTATTGAGTACAAAGTTGGGAAATTCCTGTTTGCTGCCAACA
GCAGAGCTAAGACAAATGTTGACACAGGTGGCATGGTGAAGATTATTGGGCAGAAGGCAACAGACAGAGTGCTGGGAGCA
CATATTCTGGGACCAGGCACTGCAGAAATGGTAAATGAAGCAGCTCTGGCTTTGGAATACGGAGCGTCCTGTGAAGATAT
AGCTAGAGTCTGCCATGCTCACCTGACCTTATCAGAAGCTTTTAGAGAAGCAAACTTGGCTGCATCATTTGGCAAAGTGA
TCAACTTT

Alignment

ORF - retro_cpor_685 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 94.34 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MQSWSRVYRSLAKRGHFNRISHGLQGVSAVPLRTYADQSIDADVTVVGSGPGGY--VAAIKAAQLGFKTV
          MQSW.RVYRSLAKRGHFN.ISHGLQGVSAVPLRTYADQSIDADV.V.GSGPGGY..VAAIKAAQLGFKTV
Retrocopy MQSWNRVYRSLAKRGHFNQISHGLQGVSAVPLRTYADQSIDADVKVIGSGPGGYGYVAAIKAAQLGFKTV

Parental  CVEKNETLGGTCLNVGCIPSKALLNNSHYYHMAHGKDFASRGIEMSEVRLNLEKMMEQKTNAVKALTGGI
          CVEKNE.LGGTCLNVGCIPSKALLNNSHYYHMAHGKDFASRGIEMSEVRLNLEKMMEQKTNAVKALTGGI
Retrocopy CVEKNEILGGTCLNVGCIPSKALLNNSHYYHMAHGKDFASRGIEMSEVRLNLEKMMEQKTNAVKALTGGI

Parental  AHLFKQNKVVHVNGFGKITGKNQVTATKADGGTQVIDTKNILIATGSEVTPFPGITIDEDTIVSSTGALS
          AHLFKQNKVVHVNGFGKITGKNQVTATKADG.TQ.IDTKNILIATGSE.TPFPGITIDEDTIVSSTGALS
Retrocopy AHLFKQNKVVHVNGFGKITGKNQVTATKADGSTQDIDTKNILIATGSEITPFPGITIDEDTIVSSTGALS

Parental  LKKVPEKMVVIGAGVIGVELGSVWQRLGADVTAVEFLGHVGGVGIDMEISKNFQRILQKQGFKFKLNTKV
          LKKVPEKM.VIGAGVIGVELGS.WQRLGADVTAVEFLGHVGGVGIDMEISKNFQRILQKQGFKFKLNT.V
Retrocopy LKKVPEKMFVIGAGVIGVELGSIWQRLGADVTAVEFLGHVGGVGIDMEISKNFQRILQKQGFKFKLNTNV

Parental  TGATKKSDGKIDVSIEAASGGKAEVITCDVLLVCIGRRPF-TQNLGLEELGIELDPRGRIPVNSRFQTKV
          TGATKKSDGKIDVSIEAASGGKAEVITCDVLLVCI...P..TQNLGLEELGIELDPR.RIPVNSRFQTKV
Retrocopy TGATKKSDGKIDVSIEAASGGKAEVITCDVLLVCIS--PY>TQNLGLEELGIELDPRSRIPVNSRFQTKV

Parental  PNIYAIGDVVAGPMLAHKAEDEGIICVEGMAGGAVHIDYNCVPSVIYTHPEVAWVGKSEEQLKEEGIEYK
          PNIYAIG.VVAGPMLAHKAEDEGIICVEGMAGGAVH.DY.CVPSVIYTHPEVAWVGKSEEQLKEEGIEYK
Retrocopy PNIYAIGEVVAGPMLAHKAEDEGIICVEGMAGGAVHMDYSCVPSVIYTHPEVAWVGKSEEQLKEEGIEYK

Parental  VGKFPFAANSRAKTNADTDGMVKIIGQKATDRVLGAHILGPGAGEMVNEAALALEYGASCEDIARVCHAH
          VGKF.FAANSRAKTN.DT.GMVKIIGQKATDRVLGAHILGPG..EMVNEAALALEYGASCEDIARVCHAH
Retrocopy VGKFLFAANSRAKTNVDTGGMVKIIGQKATDRVLGAHILGPGTAEMVNEAALALEYGASCEDIARVCHAH

Parental  PTLSEAFREANLAASFGKAINF
          .TLSEAFREANLAASFGK.INF
Retrocopy LTLSEAFREANLAASFGKVINF

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
SRP017611_brain	0.17 RPM	60.33 RPM
SRP017611_kidney	0.63 RPM	144.05 RPM
SRP017611_liver	0.22 RPM	57.54 RPM
SRP040447_lung	0.00 RPM	49.13 RPM
SRP040447_skeletal_muscle	0.22 RPM	174.64 RPM

ChIP-Seq

Cavia porcellus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cpor_685 retrocopy.

TSS

Cavia porcellus was not studied using FANTOM5 data.

Lab

retro_cpor_685 was not experimentally validated.

Homology

Retrocopy orthology:

Cavia porcellus 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 5 parental genes, and 6 retrocopies.

Species	Parental gene accession	Retrocopies number
Cavia porcellus	ENSCPOG00000005312	1 retrocopy	retro_cpor_685 ,
Monodelphis domestica	ENSMODG00000016316	2 retrocopies	retro_mdom_1455, retro_mdom_448,
Oryctolagus cuniculus	ENSOCUG00000014667	1 retrocopy	retro_ocun_437,
Ictidomys tridecemlineatus	ENSSTOG00000007445	1 retrocopy	retro_itri_1226,
Tursiops truncatus	ENSTTRG00000003989	1 retrocopy	retro_ttru_699,