RetrogeneDB ID: retro_cpor_1089

Retrocopy location

• Organism: Guinea Pig (Cavia porcellus)
• Coordinates: scaffold_45:3668924..3670272(-)
• Located in intron of: ENSCPOG00000001344

Retrocopy information

• Ensembl ID: ENSCPOG00000025525
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: DLST
• Ensembl ID: ENSCPOG00000009316
• Aliases: None
• Description: None

Sequence

>retro_cpor_1089
ATGCTGTCCCACTCACGCTGCGTGTTCCCAGCATTTAGCCGCTCACTCGCCACCTTCCAGAAGGGGAACTGCCCTCTAGG
GAGACGTTCCCTGCCTGGGGTCTCCTTATGTCAGGGACCAAGTTACCCTGACAGCAGGAAGATTGTCATTGACAACAGTA
GTATCTTCAGTGTTCGATATTTCAGAACCACAGCTGTGTGCAAGGATGATGTGATTACAGTCAATACCCCAGCGTTTGCA
GAATCTGTCACAGAGGGAGATGTCAGGTGGGAGAAAGCTGTTGGAGACACAGTTGCAGAAGACGAAGTGGTTTGTGAGAT
TGAAACGGATAAGACATCTGTGCAGGATCCATCACCAGCAAATGGTGTGAGAGAAGCTCTTTTGGTACCTGATGGAGGGA
AAGTTGAAGGAGGCACTCTTCTGTTCACACTCAGGAAAACTGGTGCTGCACCTGTTAAGGCCAAGCCAGCCGAAGGTCCC
CCTGCAGCCCCAAAAGCAGAACCTACAGTATCAGCAGTTCCTCCTCCCTCTGCTGCCTACTCAGATGCCACCACTGCCCT
CCCCCTCACAGCCTCCTTCTAGCAAACCAGTCTCTGCCATTAAACCCACAGCTGCACCTCCACTGGCTGATTCAGGAGCT
GGTAGGGTTCAGAACATCGGGGAAAAAATGAACAGGATGCAACAGCGAATTGCTCAGCGTCTGAAGGAGGCCCAGAATAC
ATGTGCAATACTGACTACTTTCAATGAGATTGACATGAGTAACATCCAGGAAATGAGAGCTTGGCACAAAGATGCTTTTC
TAAAGAAACATAACCTCAAACTAGGCTTTATGTCGGCATTTGTGAAGGCCTCAGCCTTTGCCTTGCAGGAGCAGCCTGTT
GTAAATGCAGTGATTGATGATGCAACCAAAGAAGTGGTGTATAGGGACTACATTGATATCAGTGTTGCAGTGACCACTCC
ACCGGGTCTGGTGGTTCCTGTCATCAGGAATGTGGAAACTATGAATTATGCAGATATTGAACGAACCATCAGTGAACTGG
GAGAGAAGGCCCGAAAGAACGAACTTGCCATTGAAGATATAGATGGTGGTACTTTCACTATTAGCAATGGAGGCGTGTTT
GGCTCACTCTTTGGAACACCCATCATCAACCCTCCTCAGTCTGCCATCCTTGGCATGCATCCCATTTTCGACAGACCAGT
GGCTGTGGGTGGCAAGGTAGAGGTGCGGCTTATGATGTATGTGGCACTGACCTACCATCACCGGCTGATTGATGGCAGAG
AGGCTGTGACTTTCCTCCGAAAAATCAAGGCAGTGGTAGAGGATCCCAGAGTTCTCTTCCTGGACCTT

Alignment

ORF - retro_cpor_1089 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 87.77 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MLSRSRCVSRAFSRSLAAFQKGNCPLGRRSLPGVSLCQGPSYPDSRKIVIDNSSIFSVRYFRTTAVCKDD
          MLS.SRCV..AFSRSLA.FQKGNCPLGRRSLPGVSLCQGPSYPDSRKIVIDNSSIFSVRYFRTTAVCKDD
Retrocopy MLSHSRCVFPAFSRSLATFQKGNCPLGRRSLPGVSLCQGPSYPDSRKIVIDNSSIFSVRYFRTTAVCKDD

Parental  VITVNTPAFAESVTEGDVRWEKAVGDTVAEDEVVCEIETDKTSVQVPSPANGVIEALLVPDGGKVEGGTP
          VITVNTPAFAESVTEGDVRWEKAVGDTVAEDEVVCEIETDKTSVQ.PSPANGV.EALLVPDGGKVEGGT.
Retrocopy VITVNTPAFAESVTEGDVRWEKAVGDTVAEDEVVCEIETDKTSVQDPSPANGVREALLVPDGGKVEGGTL

Parental  LFTLRKTGAAPVKAKPAEGPTAAPKAEPTVSAVPPPAAA-SIPTQMPPVPS-PSQPPSSKPVSAIKPTAA
          LFTLRKTGAAPVKAKPAEGP.AAPKAEPTVSAVPPP.AA.S..T...P....PS..P.S....AIKPTAA
Retrocopy LFTLRKTGAAPVKAKPAEGPPAAPKAEPTVSAVPPPSAAYSDATTALPLTA>PSSKPVS----AIKPTAA

Parental  PPLADSGAGR--GLRSEHREKMNRMRQRIAQRLKEAQNTCAMLTTFNEIDMSNIQEMRARHKDAFLKKHN
          PPLADSGAGR.............R..QR.....KEAQNTCA.LTTFNEIDMSNIQEMRA.HKDAFLKKHN
Retrocopy PPLADSGAGRVQNIGEKMNRMQQRIAQRL----KEAQNTCAILTTFNEIDMSNIQEMRAWHKDAFLKKHN

Parental  LKLGFMSAFVKASAFALQEQPVVNAVIDDATKEVVYRDYIDISVAVATPRGLVVPVIRNVETMNYADIER
          LKLGFMSAFVKASAFALQEQPVVNAVIDDATKEVVYRDYIDISVAV.TP.GLVVPVIRNVETMNYADIER
Retrocopy LKLGFMSAFVKASAFALQEQPVVNAVIDDATKEVVYRDYIDISVAVTTPPGLVVPVIRNVETMNYADIER

Parental  TISELGEKARKNELAIEDMDGGTFTISNGGVFGSLFGTPIINPPQSAILGMHAIFDRPVAVGGKVEVRPM
          TISELGEKARKNELAIED.DGGTFTISNGGVFGSLFGTPIINPPQSAILGMH.IFDRPVAVGGKVEVR.M
Retrocopy TISELGEKARKNELAIEDIDGGTFTISNGGVFGSLFGTPIINPPQSAILGMHPIFDRPVAVGGKVEVRLM

Parental  MYVALTYDHRLIDGREAVTFLRKIKAAVEDPRVLLLDL
          MYVALTY.HRLIDGREAVTFLRKIKA.VEDPRVL.LDL
Retrocopy MYVALTYHHRLIDGREAVTFLRKIKAVVEDPRVLFLDL

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	0.46 RPM	43.19 RPM
SRP017611_kidney	0.42 RPM	126.88 RPM
SRP017611_liver	0.22 RPM	46.88 RPM
SRP040447_lung	0.25 RPM	53.87 RPM
SRP040447_skeletal_muscle	0.38 RPM	147.42 RPM

ChIP-Seq

Cavia porcellus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cpor_1089 retrocopy.

TSS

Cavia porcellus was not studied using FANTOM5 data.

Lab

retro_cpor_1089 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 8 parental genes, and 8 retrocopies.

Species	Parental gene accession	Retrocopies number
Cavia porcellus	ENSCPOG00000009316	1 retrocopy	retro_cpor_1089 ,
Homo sapiens	ENSG00000119689	1 retrocopy	retro_hsap_407,
Gorilla gorilla	ENSGGOG00000011591	1 retrocopy	retro_ggor_403,
Nomascus leucogenys	ENSNLEG00000016330	1 retrocopy	retro_nleu_1006,
Oryctolagus cuniculus	ENSOCUG00000015606	1 retrocopy	retro_ocun_322,
Pan troglodytes	ENSPTRG00000006543	1 retrocopy	retro_ptro_312,
Tursiops truncatus	ENSTTRG00000001915	1 retrocopy	retro_ttru_681,
Xenopus tropicalis	ENSXETG00000013264	1 retrocopy	retro_xtro_46,