RetrogeneDB ID: retro_cjac_1756

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 19:44207552..44209074(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: PAPSS1
• Ensembl ID: ENSCJAG00000015905
• Aliases: None
• Description: None

Sequence

>retro_cjac_1756
ATGGAGATCCCCGGGAGCCTGTGCAAGAAAGTCAAGCTGAGCAAGATGCAGAGAATGCAGAGAGCAACTAATGTCACCTA
CCAAGCCCATCATATCAGCAGGAACAAGAACGGTCAGGTTGTGGGGACCAGAGGTGGCTTTCGTGGCTGCACGTTTGGCT
CACAGGCTTGTCTAGAGCCAGAAAGACTACGGTCAGCGTGGCTTTGAAGAGTACCTGGTTTGCCATGATATTGCAGGCTA
CACTCTGGATGGTGCCGATATTCGTCAAGGTCTCAATAAAAATCTAGGCTTTAGTCCTGAAGACAGAGAAGGGAATGTTC
GACACGTGGCAGAAGTTACAGAGCTATTTGCAGGCGCTGGTTTAGTGTGCATCGCAAGTTTTATGTCACCTTATAGTCAG
GATCGCCATGATGCAAGACAAATTCATGAGGGGCAAGTTCGCCGTTTTCTGAAGTATTTGTTGATGCTCCTCTGCATGTT
TGTGAACAGAGGGATGTCAAAGGACTCTCCAAAAACCCCAGCCAGGAGAAATTAAAGGTTTCACTGGGATCGATTCTGAA
GATGAAAAGCCAGAGGCCCCTGAATTGGTGCTGAAAACAGACTCCTGTGAAGACTGTGTCCAGCAAGTTGCGGAACTTCT
ACAGGAACTAGATGTTGTACCTGTAGATGCATCTCGTGAGGTAAAATAACTGTATGTGCCAGGAAATAAACTTCATTTGG
CAAAAACAGATGCAGAAATGTTACCAGCACTGAAAATTAATCAAGTGGATATGCAGTGGGTGCAGGTTTTGACAGCAGGT
TGGGGAACCCCACTGAGTGGCTTCATGAGAGAGAGGGAATAATCGCAGTGCCTTCATTTTGATTGTCTTCTGGATGGAGG
TGTCATCAACTTGTCAGTACCTATAGTTCTGACAAGTTCTGCTACTCATGAAGTTAAACAGAGGCTGGACGGCTGGACAG
CATTTACTCTGATGTATGAGGACCGCCATGTGGCCATTCTTCACAATCCAGAGTTTTATGAGCACAGGGAAGAGGAGCAC
TGTGCCAGACGGTGGGGAACAACATGCAAGAACCACCCCCACATCAGGATGGTTATGGAACAAGGAGATTGGTTGATTGG
AGGAGATCTTCAAGTCTTGGACTGAGTTTATTGCAATGATGGTCTTGATCAGTATCGTCTTACTCCTACTGAGCTAAAGC
CGATATTTAAAGATATGAATGCTGACGCTGTCTTTGCATTTCAGTTACGCAACCCAGTGCACCATGGACATGCCCTGTTA
ATGCAGCATACCCATAAGCAATTTCTAGAGAGCAGCTACTGGTCCCCATCCTCCTCCTTCACTCTCTGGGTGGCTGGACA
AAGGATGATGATGTTCCTTTGATGTGGCATTTGAAGCAGCATGCTGCAGTGTTGGAGGAAGGAGTCCTGAATCCTGAGAT
GACAGTGGTGGCCATCTTCCCGTCTCCCATGAGGTATGCCAGACCAGCTGAGGTCCATTGGCATTGCAGGAGCCAACTTT
TA

Alignment

ORF - retro_cjac_1756 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 81.5 %
• Parental protein coverage: 82.05 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 5

Retrocopy - Parental Gene Alignment:

Parental  MESPGSLCKKVKLSNNAQNWGMQRATNVTYQAHHVSRNKRGQVVGTRGGFRGCT-VWLTGLSGAGKTTVS
          ME.PGSLCKKVKLS.......MQRATNVTYQAHH.SRNK.GQVVGTRGGFRGCT.VWLTGLS.A.KTTVS
Retrocopy MEIPGSLCKKVKLSKMQR---MQRATNVTYQAHHISRNKNGQVVGTRGGFRGCT<VWLTGLSRARKTTVS

Parental  MAL-EEYLVCHGIPCYTLDGDNIRQGLNKNLGFSPEDREENVRRIAEVAKLFADAGLVCITSFISPYTQD
          .AL.EEYLVCH.I..YTLDG..IRQGLNKNLGFSPEDRE.NVR..AEV..LFA.AGLVCI.SF.SPY.QD
Retrocopy VAL<EEYLVCHDIAGYTLDGADIRQGLNKNLGFSPEDREGNVRHVAEVTELFAGAGLVCIASFMSPYSQD

Parental  RNNARQIHEG-ASLPFFEVFVDAPLHVCEQRDVKGLYK-KARAGEIKGFTGIDSEYEKPEAPELVLKTDS
          R..ARQIHEG.AS.PF.EVFVDAPLHVCEQRDVKGL.K.K...GEIKGFTGIDSE.EKPEAPELVLKTDS
Retrocopy RHDARQIHEG<ASSPFSEVFVDAPLHVCEQRDVKGLSK<KPQPGEIKGFTGIDSEDEKPEAPELVLKTDS

Parental  CDVNDCVQQVVELLQERDIVPVDASYEVKELYVPENKLHLAKTDAETLPALKINKVDMQWVQVLAEGWAT
          C...DCVQQV.ELLQE.D.VPVDAS.EVK.LYVP.NKLHLAKTDAE.LPALKIN.VDMQWVQVL..GW.T
Retrocopy CE--DCVQQVAELLQELDVVPVDASREVK*LYVPGNKLHLAKTDAEMLPALKINQVDMQWVQVLTAGWGT

Parental  PLNGFMREREYLQCLHFDCLLDGGVINLSVPIVLT--ATHEDKERLDGCTAFALMYEGRRVAILRNPEFY
          PL.GFMRERE..QCLHFDCLLDGGVINLSVPIVLT..ATHE.K.RLDG.TAF.LMYE.R.VAIL.NPEFY
Retrocopy PLSGFMRERE*SQCLHFDCLLDGGVINLSVPIVLTSSATHEVKQRLDGWTAFTLMYEDRHVAILHNPEFY

Parental  EHRKEERCARQWGTTCKNHPYIKMVMEQGDWLIGGDLQVLDRVYWNDGLDQYRLTPTELKQKFKDMNADA
          EHR.EE.CAR.WGTTCKNHP.I.MVMEQGDWLIGGDLQVLD.VY.NDGLDQYRLTPTELK..FKDMNADA
Retrocopy EHREEEHCARRWGTTCKNHPHIRMVMEQGDWLIGGDLQVLD*VYCNDGLDQYRLTPTELKPIFKDMNADA

Parental  VFAFQLRNPVHNGHALLMQDTHKQLLERGYRR-PVLLLHPLGGWTKDDDVPLMWRMKQHAAVLEEGVLNP
          VFAFQLRNPVH.GHALLMQ.THKQ.LE..Y...P.LLLH.LGGWTKDDDVPLMW..KQHAAVLEEGVLNP
Retrocopy VFAFQLRNPVHHGHALLMQHTHKQFLESSYWS<PILLLHSLGGWTKDDDVPLMWHLKQHAAVLEEGVLNP

Parental  ETTVVAIFPSPMMYAGPTEVQWHCRARMV
          E.TVVAIFPSPM.YA.P.EV.WHCR....
Retrocopy EMTVVAIFPSPMRYARPAEVHWHCRSQLL

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	33.59 RPM
SRP051959_heart	0.02 RPM	28.82 RPM
SRP051959_kidney	0.00 RPM	41.09 RPM
SRP051959_liver	0.00 RPM	14.49 RPM
SRP051959_lung	0.02 RPM	35.24 RPM
SRP051959_lymph_node	0.00 RPM	29.79 RPM
SRP051959_skeletal_muscle	0.00 RPM	9.83 RPM
SRP051959_spleen	0.00 RPM	30.76 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_1756 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_1756 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_1756 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 2 parental genes, and 2 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000015905	1 retrocopy	retro_cjac_1756 ,
Equus caballus	ENSECAG00000021678	1 retrocopy	retro_ecab_862,