RetrogeneDB ID: retro_cjac_524

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 1:46723207..46725185(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSCJAG00000021950
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: MTMR7
• Ensembl ID: ENSCJAG00000011725
• Aliases: None
• Description: None

Sequence

>retro_cjac_524
GAGCACATCGGCACGCCCAAGGCTGAAAATGTCCGCTTGGTAGATCGAGTGTCTCCTAAAAAAGCAGCTCTAGGTACTTT
GTATTTGACGGCTACTCACGTCATATTCGTTGAAAATTCACCTGACACAAGAAAAGAAACATGGATTCTTCACAGTCAGA
TTTCCACCATTGAGAAACAGGCAACAACTGCTACTGGATGCCCTCTGCTGATTCGCTGCAAGAACTTTCAGATAATACAG
CTCATCATACCTCAGGAAAGAGATTGCCATGACGTGTACATCTCCCTGATACGCCTTGCAAGGCCAGTGAAATACGAGGA
GTTATACTGCTTTTCATTTAACCCCATGCTGGATAAAGAAGAAAGAGAGCAAGGCTGGGTGCTGATCAATCTCAGTGAAG
AATACAAGCGGATGGGCCTCCCTAATAATTACTGGCTGCTCAGTGATGTGAATAGACAGTACAGAGTTTGTGACTCTTAT
CCTACTGAACTGTACGTTCCCAAATCGGCCACGGCACACATCATAGTGGGGAGTTCCAAATTCCGGAGTAGACAGCGATT
TCCTGTCCTTTCTTACTACTATAAAGATAACCACGCCTCCATCTGCCGGAGCAGCCAGCCCCTGTCTGGCTTCAGTGCCC
GGTGCCTAGAGGATGAGCAGATGCTCCAGGCCATTAGAAAAGCCAATCCAGGAAGTGACTTCGTTTATGTTGTTGACACC
CGGCCTAAACTTAATGCAATGACAAATCGTGCTGCAGGGAAAGGCTATGAGAATGAAGACAATTATTCGAATATCAAGTT
TCAGTTTATCGGGATAGAGAACATCCATGTCATGAGGAACAGTCTGCAGAAAATGCTGGAAGTGTGTGAACTTAAATCTC
CCTCCATGAGTGACTTCCTGTGGGGTCTGGAGAACTCTGGCTGGCTAAGGCACATTAAGGCCATAATGGATGCAGGAATC
TTCATTGCAAAGGCAGTTTCAGAGGAAGGGGCAAATGTGCTTGTTCACTGTTCCGACGGCTGGGACAGGACTGCTCAGGT
GTGCTCAGTGGCGAGCCTGCTGCTGGACCCGCACTACCGGACTCTGAAGGGCTTCATGGTATTAATTGAAAAGGACTGGA
TTTCCTTTGGTCATAAGTTTAATCACAGATATGGCAATCTAGACGGTGATCCAAAAGAAATCTCTCCCGTTATTGACCAG
TTCATTGAGTGTGTTTGGCAGTTAATGGAAAAATTTCCCTGTGCCTATTGAGTTCAATGAGAGGTTTTTGATTCACATTC
AACATCACATTTATTCCTGCCAGTTTGGAAACTTCCTATGTAACAGCCAAAAGGAGAGACAAGAACTCAAGATTCAAGAA
AGAACATACTCATTATGGGCTCACCTGTGGAAGAATTGGGCCGACTACCTGAATCCTCTGTTTAGAGCTGATCACAGCCA
GACCCAGGGAACCCTTCATCTCCCTACAACACCATGCAACTTTATGTACAAGTTTTGGAGTGGAATGTATAACCGCTTTG
AAAAGGGGATGCAGCCCGGACAATCAGTTACAGATTACCTGATGGCAGTGAAGGAGGAAACTCAGCAGCTAGAGGAAGAA
CTAGAGGCCTTGGAAGAGAGGCTGGAAAAAATTCAAAAGGTCCAGTTAAATTGCACTAAGGTGAAGTGTAAGCAAAGTGA
ACCCAGCAAGCACTCAGGGTTTTCTACCTCAGACAACAGCATAGCCAACACTCCCCAGGATTACAGTGGGAATCTGAAAT
CATTTCCATCCCGGAGCCCTTCGCAAGGCGATGAAGATTCTGCTCTGATTCTAACCCAAGACAATTTGAAAAGCTCAGAT
CCAGATCTGTCAGCCAACAGTGACCAGGAGTCTGGGGTGGAGGATCTGAGCTGTTGGTCTCCAAGTGGTGGTGAGCATGC
ACCAAGTGAAGATAGTGGCAAGGACCGGGACTCTGATGAAGCTGTGTTTCTCACTGCC

Alignment

ORF - retro_cjac_524 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 97.73 %
• Parental protein coverage: 99.85 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  EHIRTPKVENVRLVDRVSPKKAALGTLYLTATHVIFVENSPDTRKETWILHSQISTIEKQATTATGCPLL
          EHI.TPK.ENVRLVDRVSPKKAALGTLYLTATHVIFVENSPDTRKETWILHSQISTIEKQATTATGCPLL
Retrocopy EHIGTPKAENVRLVDRVSPKKAALGTLYLTATHVIFVENSPDTRKETWILHSQISTIEKQATTATGCPLL

Parental  IRCKNFQIIQLIIPQERDCHDVYISLIRLARPVKYEELYCFSFNPMLDKGEREQGWVLINLSEEYKRMGL
          IRCKNFQIIQLIIPQERDCHDVYISLIRLARPVKYEELYCFSFNPMLDK.EREQGWVLINLSEEYKRMGL
Retrocopy IRCKNFQIIQLIIPQERDCHDVYISLIRLARPVKYEELYCFSFNPMLDKEEREQGWVLINLSEEYKRMGL

Parental  PNNYWQLSDVNREYRVCDSYPTELYVPKSATAHIIVGSSKFRSRRRFPVLSYYYKDNHASICRSSQPLSG
          PNNYW.LSDVNR.YRVCDSYPTELYVPKSATAHIIVGSSKFRSR.RFPVLSYYYKDNHASICRSSQPLSG
Retrocopy PNNYWLLSDVNRQYRVCDSYPTELYVPKSATAHIIVGSSKFRSRQRFPVLSYYYKDNHASICRSSQPLSG

Parental  FSARCLEDEQMLQAIRKANPGSDFVYVVDTRPKLNAMANRAAGKGYENEDNYSNIKFQFIGIENIHVMRN
          FSARCLEDEQMLQAIRKANPGSDFVYVVDTRPKLNAM.NRAAGKGYENEDNYSNIKFQFIGIENIHVMRN
Retrocopy FSARCLEDEQMLQAIRKANPGSDFVYVVDTRPKLNAMTNRAAGKGYENEDNYSNIKFQFIGIENIHVMRN

Parental  SLQKMLEVCELKSPSMSDFLWGLENSGWLRHIKAIMDAGIFIAKAVSEEGASVLVHCSDGWDRTAQVCSV
          SLQKMLEVCELKSPSMSDFLWGLENSGWLRHIKAIMDAGIFIAKAVSEEGA.VLVHCSDGWDRTAQVCSV
Retrocopy SLQKMLEVCELKSPSMSDFLWGLENSGWLRHIKAIMDAGIFIAKAVSEEGANVLVHCSDGWDRTAQVCSV

Parental  ASLLLDPHYRTLKGFMVLIEKDWISFGHKFNHRYGNLDGDPKEISPVIDQFIECVWQLMEQFPCAF-EFN
          ASLLLDPHYRTLKGFMVLIEKDWISFGHKFNHRYGNLDGDPKEISPVIDQFIECVWQLME.FPCA..EFN
Retrocopy ASLLLDPHYRTLKGFMVLIEKDWISFGHKFNHRYGNLDGDPKEISPVIDQFIECVWQLMEKFPCAY>EFN

Parental  ERFLIHIQHHIYSCQFGNFLCNSQKERRELKIQERTYSLWAHLWKNRADYLNPLFRADHSQTQGTLHLPT
          ERFLIHIQHHIYSCQFGNFLCNSQKER.ELKIQERTYSLWAHLWKN.ADYLNPLFRADHSQTQGTLHLPT
Retrocopy ERFLIHIQHHIYSCQFGNFLCNSQKERQELKIQERTYSLWAHLWKNWADYLNPLFRADHSQTQGTLHLPT

Parental  TPCNFMYKFWSGMYNRFEKGMQPRQSVTDYLMAVKEETQQLEEELEALEERLEKIQKVQLNCTKVKCKQS
          TPCNFMYKFWSGMYNRFEKGMQP.QSVTDYLMAVKEETQQLEEELEALEERLEKIQKVQLNCTKVKCKQS
Retrocopy TPCNFMYKFWSGMYNRFEKGMQPGQSVTDYLMAVKEETQQLEEELEALEERLEKIQKVQLNCTKVKCKQS

Parental  EPSKHSGFSTSDNSIANTPQDYSGNLKSFPSRSPSQGDEDSALILTQDNLKSSDPDLSANSDQESGVEDL
          EPSKHSGFSTSDNSIANTPQDYSGNLKSFPSRSPSQGDEDSALILTQDNLKSSDPDLSANSDQESGVEDL
Retrocopy EPSKHSGFSTSDNSIANTPQDYSGNLKSFPSRSPSQGDEDSALILTQDNLKSSDPDLSANSDQESGVEDL

Parental  SCRSPSGGEHAPSEDSGKDRDSDEAVFLTA
          SC.SPSGGEHAPSEDSGKDRDSDEAVFLTA
Retrocopy SCWSPSGGEHAPSEDSGKDRDSDEAVFLTA

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	0.11 RPM	3.13 RPM
SRP051959_heart	0.12 RPM	4.47 RPM
SRP051959_kidney	0.09 RPM	2.55 RPM
SRP051959_liver	0.06 RPM	4.31 RPM
SRP051959_lung	0.07 RPM	4.91 RPM
SRP051959_lymph_node	0.05 RPM	2.90 RPM
SRP051959_skeletal_muscle	0.02 RPM	1.94 RPM
SRP051959_spleen	0.06 RPM	2.86 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_524 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_524 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_524 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 1 parental gene, and 1 retrocopy.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000011725	1 retrocopy	retro_cjac_524 ,