RetrogeneDB ID: retro_cjac_4167

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: X:53439934..53441472(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: PIAS2
• Ensembl ID: ENSCJAG00000008117
• Aliases: None
• Description: None

Sequence

>retro_cjac_4167
CGAGAATTGTATAGATGCCTATATCCGCGAACTCTTGAAGGACTTTCTGATTTATCCACAATCAAATCATCGGTTTTCAG
TTTGGATGGTAGATAATCACCTGTAGAACCTGACTTGGCCGTGGCTGGAATCCACTCGTTTCCTTCCACTTCAGTTACAC
CTCACTCACAATCCTCTCCTGTTGGTTCTGTGCTGCTTCAAGGTACTAAGCCCACATTTGAGATGCAGCAGCCATCTCCC
CCAATTCCTCCTGTCCATCCTGATGTGCAGTTAAAAAATCTGCCCTTTTATGATGTCCTTGATGTTCTCATCAAGCCCAC
GAGTTTAGTTCAAAGCAGTATTCAGCGATTTCAAGATAAGTTTTTTATTTTCGCTTTGAAACCTCAGCAAGTTAGAGAGA
TATGCATATCCAGGGATTTTTTGCCAGGTGGTAGGAGAGATTATACAGTACAAGTTCAGTTGAGACTTTGCCTGGCAGAA
ACAAGTTGCCCTCAAGAAGATAACTATCCAAATAGTCTATGTATACAAGTAAATGGGAAGCTATTTCCTTTGCCTGGCTA
CGCACCACCACCTAAAATAGGATTGAACAGAAGCGCCCTGGACGCCCCTTGAATATTACATCTTTAGTTAGGTTATCTTC
AGCTGTGCCAAACCAAATTTCGCTTTCTTGGGCATCAGAAATTGGGAAGAATTACTCCATGTCTGTGTATTTTGTACAAC
AGCTTACATCAGCCATGTTATTACAAAGATTAAAAATGAAAGGTATTAGAAACCCTGATCATTCCAGAGCAATAATAAAG
GAAAAACTTACTGCAGATCCTGATCGTGAAATTGCTACAACTAGCCTTCAGGTATCCTTGATGTGCCCTTTAGGAAAAAT
GAGGCTGACAATCCCATGCCGTACAGTGACTTGTACACATCTGCAGTGTTTTGATGCTGCCCTTTATCTACAAATGAATG
AGAAGAAGCCCACCTGGATTTGTCCTGTATGTGACAAAAAAGTTGCCTATGAAAGTCTAATATTAGATGGGCTTTTTATG
GAAATTTTCAATGACTATTCTGATGTGGATGAGATCAAATCCCAATAAGATGGTTCTTGGTGTCCAATGAGACCGAAGAA
AGAAGCTGTGAAAGTATCCAGCCAACCGTGCACAAAAATAGAAAGTTCAAGTGTCCTCAGTAAGTTCAGTGACCGTAGCC
AGTGAGGCAAGCAAGAAGAAAGTAGATGTTATTGATCTTACAATAGAAAGCTCTTCTGATGAAGAGGAAGACCCTCCTGC
CAAAAGGAAATGCATCTTTATGTCAGAAACACAAAGCACCCAACCACAGGGGTTCTCATGTATCAGCTATCTTCTGTAAG
GGTGCCCAGTGTGACCTTGGTTGATCCTGCTGCTATTCCACCTTCATTAACAGACTACTCAGTACCATTCCACCACATGC
CAATATCAAGCATGTCATCAGATTTGCCAGGAGAACAAAGAAGAAATGATATTAATAATGAACTGGCGCTTGGAAAATCT
TCTGATACCATGCAACAG

Alignment

ORF - retro_cjac_4167 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 88.42 %
• Parental protein coverage: 90.03 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  RELYRRRYPRTLEGLSDLSTIKSSVFSLDGSSSPVEPDLAVAGIHSLPSTSVTPHSPSSPVGSVLLQDTK
          RELYR..YPRTLEGLSDLSTIKSSVFSLDG..SPVEPDLAVAGIHS.PSTSVTPHS.SSPVGSVLLQ.TK
Retrocopy RELYRCLYPRTLEGLSDLSTIKSSVFSLDGR*SPVEPDLAVAGIHSFPSTSVTPHSQSSPVGSVLLQGTK

Parental  PTFEMQQPSPPIPPVHPDVQLKNLPFYDVLDVLIKPTSLVQSSIQRFQEKFFIFALTPQQVREICISRDF
          PTFEMQQPSPPIPPVHPDVQLKNLPFYDVLDVLIKPTSLVQSSIQRFQ.KFFIFAL.PQQVREICISRDF
Retrocopy PTFEMQQPSPPIPPVHPDVQLKNLPFYDVLDVLIKPTSLVQSSIQRFQDKFFIFALKPQQVREICISRDF

Parental  LPGGRRDYTVQVQLRLCLAETSCPQEDNYPNSLCIKVNGKLFPLPGYAPPPK-NGIEQKRPGRPLNITSL
          LPGGRRDYTVQVQLRLCLAETSCPQEDNYPNSLCI.VNGKLFPLPGYAPPPK.N.IEQKRPGRPLNITSL
Retrocopy LPGGRRDYTVQVQLRLCLAETSCPQEDNYPNSLCIQVNGKLFPLPGYAPPPK<NRIEQKRPGRPLNITSL

Parental  VRLSSAVPNQISISWASEIGKNYSMSVYLVRQLTSAMLLQRLKMKGIRNPDHSRALIKEKLTADPDSEIA
          VRLSSAVPNQIS.SWASEIGKNYSMSVY.V.QLTSAMLLQRLKMKGIRNPDHSRA.IKEKLTADPD.EIA
Retrocopy VRLSSAVPNQISLSWASEIGKNYSMSVYFVQQLTSAMLLQRLKMKGIRNPDHSRAIIKEKLTADPDREIA

Parental  TTSLRVSLMCPLGKMRLTIPCRAVTCTHLQCFDAALYLQMNEKKPTWICPVCDKKAAYESLILDGLFMEI
          TTSL.VSLMCPLGKMRLTIPCR.VTCTHLQCFDAALYLQMNEKKPTWICPVCDKK.AYESLILDGLFMEI
Retrocopy TTSLQVSLMCPLGKMRLTIPCRTVTCTHLQCFDAALYLQMNEKKPTWICPVCDKKVAYESLILDGLFMEI

Parental  LNDCSDVDEIKFQEDGSWCPMRPKKEAMKVSSQLCTKIESSSVLSK-PCSVTVASEASKKKVDVIDLTIE
          .ND.SDVDEIK.Q.DGSWCPMRPKKEA.KVSSQ.CTKIESSSVLSK....V.......K..V........
Retrocopy FNDYSDVDEIKSQ*DGSWCPMRPKKEAVKVSSQPCTKIESSSVLSK>SVTVASEASKKKVDVIDLTIESS

Parental  SSSDEEEDPPAKRKCIFMSETQSS-PTKGVLMYQPSSVRVPSVTSVDPAAIPPSLTDYSVPFHHTPISSM
          S...E..DPPAKRKCIFMSETQS..PT.GVLMYQ.SSVRVPSVT.VDPAAIPPSLTDYSVPFHH.PISSM
Retrocopy SDEEE--DPPAKRKCIFMSETQST<PTTGVLMYQLSSVRVPSVTLVDPAAIPPSLTDYSVPFHHMPISSM

Parental  SSDLPGEQRRNDINNELALGTSSDTVQQ
          SSDLPGEQRRNDINNELALG.SSDT.QQ
Retrocopy SSDLPGEQRRNDINNELALGKSSDTMQQ

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	0.00 RPM	14.82 RPM
SRP051959_heart	0.00 RPM	36.64 RPM
SRP051959_kidney	0.00 RPM	28.38 RPM
SRP051959_liver	0.00 RPM	16.44 RPM
SRP051959_lung	0.05 RPM	24.37 RPM
SRP051959_lymph_node	0.00 RPM	22.49 RPM
SRP051959_skeletal_muscle	0.04 RPM	27.14 RPM
SRP051959_spleen	0.00 RPM	27.67 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_4167 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_4167 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_4167 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 3 parental genes, and 3 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000005911	1 retrocopy	retro_chof_549,
Callithrix jacchus	ENSCJAG00000008117	1 retrocopy	retro_cjac_4167 ,
Gallus gallus	ENSGALG00000001843	1 retrocopy	retro_ggal_24,