RetrogeneDB ID: retro_cpor_1508

Retrocopy location

• Organism: Guinea Pig (Cavia porcellus)
• Coordinates: scaffold_9:55453939..55455443(-)
• Located in intron of: ENSCPOG00000015520

Retrocopy information

• Ensembl ID: None
• Aliases: None
• Status: NOVEL

Parental gene information

• Parental gene symbol: THOC5
• Ensembl ID: ENSCPOG00000010974
• Aliases: None
• Description: None

Sequence

>retro_cpor_1508
CTCCGCAAGGCTGAAGTCACCATGAGAGACCCTCACCAACAAACCTTGGTGTTTCTGGACTGGGAGCTGGAGCAGTGAAA
AACACTGGCAGCGAAGGGCCAAGAGTATCTGTCTAACATGGAGAAAATCCTCAAAGAGATTGAGGTTTTGAAGGAGTACT
TGAGCAGTCTTGAGCCTCAGCTCAGTAGCACCATGCAGGCTTCCCTTCCAGTGCAGGAGTACCTGTTCATGCCATTTGAC
CAGGCTCACAAGCAATATGAGACAGCCAGACATCTGCCACCTCCCCTCTACATACTCCTTCTGCAGGCCACCATTTATGG
GCAGGCCTGTGATAAGACCTTGGCTGTGATCATCAGTGGCAGAGTTGATAAAACAAAAGCTCTGTTCAAGCTTCCTAACA
ACTCCCAAGATGACAAGAGTGGCTCAGATGCTGAGGAGCAGACCATGAAGCAACGGATACCCACCTTAGGAGTTCAGTGC
AAGGAGATGCTAAAGAGACATTGTCTGTCTGTCATGGTTGACCTGAAATGTAAAGAAGATAACATACTTTACCTGACTTT
CTATTACCTCATGAACCTCAGCATCCCATCTGTGAAAATCAAAGTGTCATGGAGCTGATCACCTCCCTCCATGCAGGGGA
CTTACTATCCCCTGAGCTCGGTGCTGAGCTCTTTGTATCCTGGTGATCATGCAAAGAAAACTCCAAATCAGCCAATATTA
CCAGTTTGATAAAGTTGGCGTTTTAACTTTGAGAGAATATGTATTTGACCTAGGTCATCACTATTTGTGGGTACAGAAGC
TGGGAGGCCTCCACTTCCCCAAAGAGCAACCCCAGCACACAGTGATGGCTGATCATTCGCTGAGCGCCAGCCACGTGGAA
ACAAGCATGAAGCTGCTGAAGTCCAAGGTGCAGTCCCAGTTGACCCTCCACAAACAGTTTGTGTCCTTGGAACACATCAT
TGTCCTGGTTACCAGTGATTTCCAATACCTCTTCCCTGCCCAAGTTGCCTCTTGCCTGGTGAAGTGGGTGACAATTGTCC
ATGATGATTATATGGAATTGCATTACACCAAGGACACTGTGGAAGCAGGACTAGCTGGGGACACCAATCTTTACTACATG
GCTCTCAGTGAGGGGGCATGACCCAAACTCCAGACCGCTATGGTATCGAACTCTGGCTACCCCTCTGTCCCAACTATTTT
CTAGCACTGTCTGAATTGGAAGAGAGAAAAAACCAACAGCAGTGATGACAACATTCGGGCCATGGAGAGTGAGGTCAGTG
TGCACTACAAGGAGCTCTGTGGCCTTCAGCCCAGTCACCAGCTCTTGACCAACCAGCTGCAGTGGCTATGCATGCTTCTA
GAAGTCTACCTAGAGACTGAGAGCCACAATGACAATGTGGCAGGACCCAAGAAATTTCCCCAGAAGATGTGTCTGGGGCT
TTTCAGGGGTCCAAGTAGGATGAAGCCATTAAAATATAACCATCCTCAGGGATTCTTCAGCCAC

Alignment

ORF - retro_cpor_1508 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 75.49 %
• Parental protein coverage: 74.67 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  ISKAEVTMGDPHQQTLARLDWELEQRKRLAEKYRECLSNKEKILKEIEVKKEYLSSLQPRLNSIMQASLP
          ..KAEVTM.DPHQQTL..LDWELEQ.K.LA.K..E.LSN.EKILKEIEV.KEYLSSL.P.L.S.MQASLP
Retrocopy LRKAEVTMRDPHQQTLVFLDWELEQ*KTLAAKGQEYLSNMEKILKEIEVLKEYLSSLEPQLSSTMQASLP

Parental  VQEYLFMPFDQAHKQYETARHLPPPLYVLFVQATAYGQACDKTLSVAIEGSVDEAKALFKPPDDSQDDES
          VQEYLFMPFDQAHKQYETARHLPPPLY.L..QAT.YGQACDKTL.V.I.G.VD..KALFK.P..SQDD.S
Retrocopy VQEYLFMPFDQAHKQYETARHLPPPLYILLLQATIYGQACDKTLAVIISGRVDKTKALFKLPNNSQDDKS

Parental  DSDAEEEQTTKRRRPTLGVQLDDKRKEMLKRHPLSVMVDLKCKDDSVLHLTFYYLMNLNILTVKAKVTTA
          .SDAEE.QT.K.R.PTLGVQ.....KEMLKRH.LSVMVDLKCK.D..L.LTFYYLM..N......K....
Retrocopy GSDAEE-QTMKQRIPTLGVQC----KEMLKRHCLSVMVDLKCKEDNILYLTFYYLM--NLSIPSVKIKVS

Parental  -TELITPISAGDLLSPD-SVLSCLYPGDHG-KKTPNPAN-QYQFDKVGILTLRDYVLDLGHPYLWVQKLG
          ..ELIT...AGDLLSP..SVLS.LYPGDH..K.....AN..YQFDKVG.LTLR.YV.DLGH.YLWVQKLG
Retrocopy <MELITSLHAGDLLSPE>SVLSSLYPGDHA<KENSKSAN<YYQFDKVGVLTLREYVFDLGHHYLWVQKLG

Parental  GLHFPKEQPQHTVIADHSLSASHMETTMKLLKTRVQSRLALHKQFASLEHGIVPVTSDCQYLFPAKVVSR
          GLHFPKEQPQHTV.ADHSLSASH.ET.MKLLK..VQS.L.LHKQF.SLEH.IV.VTSD.QYLFPA.V.S.
Retrocopy GLHFPKEQPQHTVMADHSLSASHVETSMKLLKSKVQSQLTLHKQFVSLEHIIVLVTSDFQYLFPAQVASC

Parental  LVKWVTIVHEDYMELHYTKDIVEAGLAGDTNLYYLALIERGTAKLQAAVVLNPGYSSIPPIFQLCLNWKG
          LVKWVTIVH.DYMELHYTKD.VEAGLAGDTNLYY.AL.E....KLQ.A.V.N.GY.S.P.IF..CLNWK.
Retrocopy LVKWVTIVHDDYMELHYTKDTVEAGLAGDTNLYYMALSEGA*PKLQTAMVSNSGYPSVPTIF*HCLNWKR

Parental  EKTNSNDDNIRAMESEVNVCYKELCGPRPSHQLLTNQLQRLCVLLDVYLETESHDDSVEGPKEFPQEKMC
          EKTNS.DDNIRAMESEV.V.YKELCG..PSHQLLTNQLQ.LC.LL.VYLETESH.D.V.GPK.FPQ.KMC
Retrocopy EKTNSSDDNIRAMESEVSVHYKELCGLQPSHQLLTNQLQWLCMLLEVYLETESHNDNVAGPKKFPQ-KMC

Parental  LRLFRGPSRMKPFKYNHPQGFFSH
          L.LFRGPSRMKP.KYNHPQGFFSH
Retrocopy LGLFRGPSRMKPLKYNHPQGFFSH

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	0.00 RPM	35.43 RPM
SRP017611_kidney	0.00 RPM	34.76 RPM
SRP017611_liver	0.00 RPM	20.59 RPM
SRP040447_lung	0.00 RPM	52.38 RPM
SRP040447_skeletal_muscle	0.00 RPM	41.89 RPM

ChIP-Seq

Cavia porcellus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cpor_1508 retrocopy.

TSS

Cavia porcellus was not studied using FANTOM5 data.

Lab

retro_cpor_1508 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
Callithrix jacchus	ENSCJAG00000019894	2 retrocopies	retro_cjac_1965, retro_cjac_2647,
Cavia porcellus	ENSCPOG00000010974	1 retrocopy	retro_cpor_1508 ,
Felis catus	ENSFCAG00000004247	1 retrocopy	retro_fcat_1394,
Myotis lucifugus	ENSMLUG00000012135	1 retrocopy	retro_mluc_2536,
Tursiops truncatus	ENSTTRG00000000542	1 retrocopy	retro_ttru_1315,