RetrogeneDB ID: retro_cjac_2647

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 5:102069836..102071558(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: THOC5
• Ensembl ID: ENSCJAG00000019894
• Aliases: None
• Description: None

Sequence

>retro_cjac_2647
ATGTCATCAGAATCAAGCAAAAAATGGAAGCCCAAAGTGATCCGAAGCGATGGAGCCCCAGCTGAAGGAAAGCAGAATCG
ATCTGACACCGAGCAGGAAGGTAAATACTACAGTGAGGAAGCCGAGGTGGATCTGTGGGACCCTGGCAGAGACTATGAGT
TATACAAGGACACCTGCCAGGAGCTACAGAGGCTGATGGCTGAGATCCAAGACCTGAAGAGCAGGGGTGGCAAGGATGTG
GCAATTGAAATAGAAGAACGGAGGATCCAGAGCTGTGTGCATTTCATGACTTTGAAAAAGCTTAACTGATTAGCCCACAT
CAGGTTGAAGAAAGGAAGAGATCAGACCCATGAGGCTAAGCAGAAAGTAGATGCCTATCACCTGCAGCTCCAGAACCTGT
TGTATGAGGTGATGGACCTTCAGGAGATCACCAAATGTTTGGAGTTTAAGTCAAAGCATGAAGAAATTGATCTGGTCAGT
TTAGAGGAGTTTTATAAGGAGTCTCCACCAGATATCAGCAAGGCTGAAGTCACCATGGGAGACCCTCACCAGCAAATACT
GGCACACCTGGACTGGGAGCTAGAGCAGCATAAAAGGCTGGCAGAGAAGTACTGTGAATGCCTATCGAACAAGGAGAAGA
TCCTCAAAGAAATTGAGGTGAAGAAGGAATACCTGAGCAGCCTCCAGCCTCGCCTCCACAGCATCATGCAGGCTTCCCTT
CTGGTGCAGGAGTACCTATTTATGCCATTTGACCAGGCTCACAAGCAGTATGAGACAGCCAGGCACCTGCCGCCTCCCCT
ATATGTCCTCTTTGTTCAGGCCACTGCATATGGGCAGGCCTGTGATAAGACGTTATCTGTGGCAATTGAAGGCAGAGTGG
ATGAAGCCAAGACTCTGTTCAAGCCTCCAGAGGACTCCCAAGATGACGAGAGTGACTCAGATGCTGAGGAGGAGTAGACC
ACAAAACGTTGGAGACCCATACTGGGGGTTTAGTTGGATGACAAACTCAAGGAGATACTGAAGAGACACCCACTGTCCGT
CATGCTTGACCTAAAGTGCAAAGATGACAGTGTGCTTCACCTGACTTTCTTCTACCTCATGAACCTCAACATCATGACAG
TAAAAGCCAAAGTGACAACTGCCACGGAGCTGATCACCCCCATCAGTGCAGGTGACTTGCTGTCTCCTGACTCAGTCCTG
AGTTGCTTGTATCTTGGGGATCATGGAAAGAAAACTCCGAATCCAGCCAATCAGTATCAGTTTGATAAAGTTGGCATCCT
GACTTTGAGTGACTACGTACTCGAGTTAGGTCACCCCTATTTGTGGGTACAGAAGCTAGGTGGTCTCCACTTCCCCAAAG
AGCAGCCCCAGCAAACAGTGATTGCTGACCACTCGCTGAGCACCAGCCACATGGAGACCACAATGAAACTTCTGAAGACC
AGGGTGCAGTCCCACCTGGCCCTCCACAAACAGTTTGCATGCCTAGAATGTGGCATTGTGCCAGTTACCAGTGATTGCCA
GTACCTCTTCCCTGCCAAGGTTGTCTCTCACCTGGTGAAGTGGGTGACAGTTGCCCATGAGGATTACACGGAGCTGCATT
TCACCAAAGACACTGTGGATGTGGGGCTGGCTGGGGACACTACTCATCGAAAGCGGCACAGCCAAACTGCAGGCTGGTGT
GGTATTGAACCCTGGCTGCTCCTCCATCCCACCTATTTTTCA

Alignment

ORF - retro_cjac_2647 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 90.43 %
• Parental protein coverage: 84.19 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MSSESSKKRKPKVIRSDGAPPEGKRNRSDTEQEGKYYSEEAEMDLRDPGRDYELYKYTCQELQRLMAEIQ
          MSSESSKK.KPKVIRSDGAP.EGK.NRSDTEQEGKYYSEEAE.DL.DPGRDYELYK.TCQELQRLMAEIQ
Retrocopy MSSESSKKWKPKVIRSDGAPAEGKQNRSDTEQEGKYYSEEAEVDLWDPGRDYELYKDTCQELQRLMAEIQ

Parental  DLKSRGGKDVAIEIEERRIQSCVHFMTLKKLNRLAHIRLKKGRDQTHEAKQKVDAYHLQLQNLLYEVMHL
          DLKSRGGKDVAIEIEERRIQSCVHFMTLKKLN.LAHIRLKKGRDQTHEAKQKVDAYHLQLQNLLYEVM.L
Retrocopy DLKSRGGKDVAIEIEERRIQSCVHFMTLKKLN*LAHIRLKKGRDQTHEAKQKVDAYHLQLQNLLYEVMDL

Parental  QKEITKCLEFKSKHEEIDLVSLEEFYEEAPPDISKAEVTMGDPHQQTLARLDWELEQRKRLAEKYCECLS
          Q.EITKCLEFKSKHEEIDLVSLEEFY.E.PPDISKAEVTMGDPHQQ.LA.LDWELEQ.KRLAEKYCECLS
Retrocopy Q-EITKCLEFKSKHEEIDLVSLEEFYKESPPDISKAEVTMGDPHQQILAHLDWELEQHKRLAEKYCECLS

Parental  NKEKILKEIEVKKEYLSSLQPRLNSIMQASLPVQEYLFMPFDQAHKQYETARHLPPPLYVLFVQATAYGQ
          NKEKILKEIEVKKEYLSSLQPRL.SIMQASL.VQEYLFMPFDQAHKQYETARHLPPPLYVLFVQATAYGQ
Retrocopy NKEKILKEIEVKKEYLSSLQPRLHSIMQASLLVQEYLFMPFDQAHKQYETARHLPPPLYVLFVQATAYGQ

Parental  ACDKTLSVAIEGSVDEAKALFKPPEDSQDDESDSDAEEEQTTKRRRPTLGVQLDDKRKEMLKRHPLSVML
          ACDKTLSVAIEG.VDEAK.LFKPPEDSQDDESDSDAEEE.TTKR.RP.LGV.LDDK.KE.LKRHPLSVML
Retrocopy ACDKTLSVAIEGRVDEAKTLFKPPEDSQDDESDSDAEEE*TTKRWRPILGV*LDDKLKEILKRHPLSVML

Parental  DLKCKDDSVLHLTFFYLMNLNIMTVKAKVTTATELITPISAGDLLSPDSVLSCLYPGDHGKKTPNPANQY
          DLKCKDDSVLHLTFFYLMNLNIMTVKAKVTTATELITPISAGDLLSPDSVLSCLY.GDHGKKTPNPANQY
Retrocopy DLKCKDDSVLHLTFFYLMNLNIMTVKAKVTTATELITPISAGDLLSPDSVLSCLYLGDHGKKTPNPANQY

Parental  QFDKVGILTLSDYVLELGHPYLWVQKLGGLHFPKEQPQQTVIADHSLSASHMETTMKLLKTRVQSRLALH
          QFDKVGILTLSDYVLELGHPYLWVQKLGGLHFPKEQPQQTVIADHSLS.SHMETTMKLLKTRVQS.LALH
Retrocopy QFDKVGILTLSDYVLELGHPYLWVQKLGGLHFPKEQPQQTVIADHSLSTSHMETTMKLLKTRVQSHLALH

Parental  KQFASLEHGIVPVTSDCQYLFPAKVVSRLVKWVTVAHEDYMELHFTKDIVDAGLAGDTNLYYMALVERGT
          KQFA.LE.GIVPVTSDCQYLFPAKVVS.LVKWVTVAHEDY.ELHFTKD.VD.GLAGDT..........G.
Retrocopy KQFACLECGIVPVTSDCQYLFPAKVVSHLVKWVTVAHEDYTELHFTKDTVDVGLAGDTTHRKRHSQTAGW

Parental  AKLQAAVVLNPGYSS
          ........L.P.Y.S
Retrocopy CGIEPWLLLHPTYFS

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
SRP051959_colon	0.02 RPM	23.72 RPM
SRP051959_heart	0.04 RPM	26.61 RPM
SRP051959_kidney	0.04 RPM	31.73 RPM
SRP051959_liver	0.06 RPM	30.95 RPM
SRP051959_lung	0.02 RPM	31.88 RPM
SRP051959_lymph_node	0.02 RPM	38.70 RPM
SRP051959_skeletal_muscle	0.04 RPM	44.86 RPM
SRP051959_spleen	0.04 RPM	34.98 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_2647 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_2647 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_2647 has 0 orthologous retrocopies within eutheria group .

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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,