RetrogeneDB ID: retro_cjac_1965

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 2:142233488..142235359(-)
• Located in intron of: ENSCJAG00000015673

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_1965
CAGGAGCTACAGAGGCTGATAGCTGAGATCTAAGACATGAAGAGTGGGGGTGGCAAGGATGTGGCAATTGAAATAGAAGA
ACAGAGGATCCAGAGCTGTGTGCATTTCATGACTTTGAGAAAGCTTAACCGATTAGCCCACATCAGGTTGAAGAAAGGAA
GAGATCAGACCCATGAGGCTAAGCAGAAAGTAAATGTCTATCACCTGCAGTTCCAGAACCTGTTGTATGAGGTGATGCAC
CTACAGAAGGAGATCACCAAATGTTTGGAGTTTAAGTCAAAGCATGAAGAAATTTATCGGGTAAGTTTAGAGGAGTTTTA
TAAGGAGGCTCCACAAGATATCAGCAAGGCTGAAGTCACCGTGGGAGACCCTCACCAGCAAACACTTGCACGTCTGGACT
GGGAGCTGGAGCAGTGTGAAAGGCTGTCAGAGGAGTACCGTGAATGCCTATCCAACAAGGAGAAGATCCTCAAGGAAATT
GAGGTGAAGAAGGAGTACCTGAGCAGTCTCCAGCTGTGCCTCAACAGCATCATGCAGGCTTCCCTTCCAGTGCAGGAGGA
CCTGTTTATGCCATTTGACCAGGCTCACAAGCAGTATGAGACAGCCAGGTACCTGCCGCCTCCCTTCTATGTCCTTTCTG
TTCAGGCCACTGCATATGGGCAGGTCTGTGATAAGACATTATCTGTGGCAATTGAAGGAAGAGTGGACAAAGCCAAGGCT
CTGTTTAAGCCTCCAGAGGACTCCCAAGATGACGAGAGTGACTCGGATGCTGAGGAGGAGCAGACCACGAAACACTGGAG
ACCCACGCTGGGGATTCAGCTGGATGACAAACACAAGGAGATGCAGACGAGTCACCCACCATCCGTCATGCTTGACCTGA
AGTGCAAAGATGACAGTGTGCTTCACCTGACTTTCTTCTACCTCATGAACCTCAATATCATGACAGTAAAAGCCAAAGTG
ACAACTGCCATGGAGCTGATCATCCCCATCAGTGCAGGTGACTTGCTGTCTCCTGACTTAGTCCTGAGTTGCTTGTATCC
TGGGGATCATGGAAAAAAACCTCCAAATCCAGCCAATCAGTGTTAGTTTGATAAAGTTGGCATCCTGACTTTGAGCAACT
ATGTACTTGAGTTAGGTCACTCCTATTTATGGGTACAGAAGCTGGATGGCCTCCACTTTCCCAAAGAGCAGTGCCAGCAA
ACAGTGATTTCTGGCCACTCACTGAGTGCCAGCCACATGGAGACCACCATGAAACTTCAGAAGAACAGGGTGCAGTCCCA
CCTGGCCCTCCACAAACAGTTTTTATCCCTAGAACATGGCATTGTGCCAGTTACCAGTGATTGCCAGTACCTCTTCCCTG
CCAAGGTTGTCTCTCGCCTGGTGAAGTGGATGACAGTTTCTCATGAGGATTACATGGAGCTGCATTTCACTAAAGACATT
GTGGATATGGGGCTGGCTGGGGGCACCAATCTCTACTACATGGCAGTCATCAAAAGGAGCAGAGCCACACTGCAGGCTGC
TGTGGTGTTGTACCCTGGCTACTTCTCCATCCCACATATTTTTCAGCTCTGTTTGAACTGGAAAGGGGAGAAAACAAACA
GCAATGAGACAACATTCAGGCCATGGAGAGCGAAGTCAATGTTTGCTGCAAGGAGCTGTGTGGCCCTTGGCCCAGCCACC
AGCTGTTGACTAACCATCTGCAGCAGCTGTGTGTGCTGCTGGATGTTTATCTGGAGACCGAGAACCATGACGACAGTGTG
GAAGGACCGAAGGAACTGCCCCAGGAGAAGATGTGTCTGCAGCTCTTCAGGGATCCTGGCAGGATGAAGCCGTTTAAATA
CAACCATCCTCAGGGATTCTTCAGCCATCGC

Alignment

ORF - retro_cjac_1965 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 87.84 %
• Parental protein coverage: 91.36 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  QELQRLMAEIQDLKSRGGKDVAIEIEERRIQSCVHFMTLKKLNRLAHIRLKKGRDQTHEAKQKVDAYHLQ
          QELQRL.AEI.D.KS.GGKDVAIEIEE.RIQSCVHFMTL.KLNRLAHIRLKKGRDQTHEAKQKV..YHLQ
Retrocopy QELQRLIAEI*DMKSGGGKDVAIEIEEQRIQSCVHFMTLRKLNRLAHIRLKKGRDQTHEAKQKVNVYHLQ

Parental  LQNLLYEVMHLQKEITKCLEFKSKHEEIDLVSLEEFYEEAPPDISKAEVTMGDPHQQTLARLDWELEQRK
          .QNLLYEVMHLQKEITKCLEFKSKHEEI..VSLEEFY.EAP.DISKAEVT.GDPHQQTLARLDWELEQ..
Retrocopy FQNLLYEVMHLQKEITKCLEFKSKHEEIYRVSLEEFYKEAPQDISKAEVTVGDPHQQTLARLDWELEQCE

Parental  RLAEKYCECLSNKEKILKEIEVKKEYLSSLQPRLNSIMQASLPVQEYLFMPFDQAHKQYETARHLPPPLY
          RL.E.Y.ECLSNKEKILKEIEVKKEYLSSLQ..LNSIMQASLPVQE.LFMPFDQAHKQYETAR.LPPP.Y
Retrocopy RLSEEYRECLSNKEKILKEIEVKKEYLSSLQLCLNSIMQASLPVQEDLFMPFDQAHKQYETARYLPPPFY

Parental  VLFVQATAYGQACDKTLSVAIEGSVDEAKALFKPPEDSQDDESDSDAEEEQTTKRRRPTLGVQLDDKRKE
          VL.VQATAYGQ.CDKTLSVAIEG.VD.AKALFKPPEDSQDDESDSDAEEEQTTK..RPTLG.QLDDK.KE
Retrocopy VLSVQATAYGQVCDKTLSVAIEGRVDKAKALFKPPEDSQDDESDSDAEEEQTTKHWRPTLGIQLDDKHKE

Parental  MLKRHPLSVMLDLKCKDDSVLHLTFFYLMNLNIMTVKAKVTTATELITPISAGDLLSPDSVLSCLYPGDH
          M...HP.SVMLDLKCKDDSVLHLTFFYLMNLNIMTVKAKVTTA.ELI.PISAGDLLSPD.VLSCLYPGDH
Retrocopy MQTSHPPSVMLDLKCKDDSVLHLTFFYLMNLNIMTVKAKVTTAMELIIPISAGDLLSPDLVLSCLYPGDH

Parental  GKKTPNPANQYQFDKVGILTLSDYVLELGHPYLWVQKLGGLHFPKEQPQQTVIADHSLSASHMETTMKLL
          GKK.PNPANQ..FDKVGILTLS.YVLELGH.YLWVQKL.GLHFPKEQ.QQTVI..HSLSASHMETTMKL.
Retrocopy GKKPPNPANQC*FDKVGILTLSNYVLELGHSYLWVQKLDGLHFPKEQCQQTVISGHSLSASHMETTMKLQ

Parental  KTRVQSRLALHKQFASLEHGIVPVTSDCQYLFPAKVVSRLVKWVTVAHEDYMELHFTKDIVDAGLAGDTN
          K.RVQS.LALHKQF.SLEHGIVPVTSDCQYLFPAKVVSRLVKW.TV.HEDYMELHFTKDIVD.GLAG.TN
Retrocopy KNRVQSHLALHKQFLSLEHGIVPVTSDCQYLFPAKVVSRLVKWMTVSHEDYMELHFTKDIVDMGLAGGTN

Parental  LYYMALVERGTAKLQAAVVLNPGYSSIPPIFQLCLNWKGEKTNSND-DNIRAMESEVNVCYKELCGPWPS
          LYYMA...R..A.LQAAVVL.PGY.SIP.IFQLCLNWKGEKTNSN..DNI.AMESEVNVC.KELCGPWPS
Retrocopy LYYMAVIKRSRATLQAAVVLYPGYFSIPHIFQLCLNWKGEKTNSNE<DNIQAMESEVNVCCKELCGPWPS

Parental  HQLLTNQLQRLCVLLDVYLETESHDDSVEGPKEFPQEKMCLRLFRGPSRMKPFKYNHPQGFFSHR
          HQLLTN.LQ.LCVLLDVYLETE.HDDSVEGPKE.PQEKMCL.LFR.P.RMKPFKYNHPQGFFSHR
Retrocopy HQLLTNHLQQLCVLLDVYLETENHDDSVEGPKELPQEKMCLQLFRDPGRMKPFKYNHPQGFFSHR

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	0.67 RPM	23.72 RPM
SRP051959_heart	0.44 RPM	26.61 RPM
SRP051959_kidney	0.75 RPM	31.73 RPM
SRP051959_liver	0.74 RPM	30.95 RPM
SRP051959_lung	0.75 RPM	31.88 RPM
SRP051959_lymph_node	1.28 RPM	38.70 RPM
SRP051959_skeletal_muscle	0.52 RPM	44.86 RPM
SRP051959_spleen	0.78 RPM	34.98 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_1965 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_1965 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_1965 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,