RetrogeneDB ID: retro_cjac_2490

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 4:159185064..159186508(-)
• Located in intron of: ENSCJAG00000003587

Retrocopy information

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

Parental gene information

• Parental gene symbol: HDAC1
• Ensembl ID: ENSCJAG00000000970
• Aliases: None
• Description: histone deacetylase 1 [Source:HGNC Symbol;Acc:4852]

Sequence

>retro_cjac_2490
ATGGCGCAGATGCAGGGCACCTGGCGGAAAGTCTGTTACTACTACGACGGGGATGTTGGAAATTACTATTATGGACAAGG
CCACCCAATGAAGCCTCACCGAATCCGCATGACTCATAATTTGCTGCTCAACTATGGTCTCTACCAAAAAATGGAAATCT
ATCGCCCTCACAAAGCCAATGCTGAGGAGATGACCAAGTACCACAGCGATGACTACATTAAATTCTTGCGCTCCATCCGT
CCAGATAACATGTCCGAGTACAGCAAGCAGATGCAGAGATTCAACGTTGGTGAGGACTGTCCAGTATTCGATGGCCTGTT
TGAGTTCTGTTAGTTGTCTACTGGTGGTTCTGTGGCAAGTGCTGTGAAACTTAATAAGCAGCAGATGGACATCGCTGTGA
ATTGGGCTGGGGGCCTGCACCATGCAAAGAAGTTCGAGGCATCTGGCTTCTGTTACGTCAATGATACTGTCTTGGCCATC
CTGGAACTGCTAAAGTATCACCAGAGGGTGCTGTATATTGACATTGATATTCACCATGGCGACGGTGTGGAAGAGGCCTT
CTATACCACAGACCGGGTCATGACTGTGTCCTTTCATAAGTATGGAGAGTACTTCCCAGGAACTGGGGACCTACGGGATA
TCGGGGCTGGCAAAGGCAAGTATTATGCTATTAACTGCCCGCTCCAAGATGGGATTGATAACGAGTCCTATGAGGCCATT
TTCAAGCCAGTCATGTCCAAAGTAATGGAGATGTTCCAGCCTAGTGCCGTGGTCTTACAGTGTGGCTCAGACTCCCTATC
TGGGGATCGGTTAGGTTGCTTCAATCTGACCATCACAGGGCACGCCAAGTGTGTGGAATTTGTCAAGAGCTTTAACCTGC
CCATGCTGATGCTGGGAGGAGGTGGTTACACCATTCGTAATGTTGCCCAATGCTGGACGTATGAGACAGCTGTGGCCCTG
GATACGGAGATGCCTAATGAGCTTCCATACAACGACTACTTCGAATACTTTGGACCAGATTTCAAGCTCCACATCAGTCC
TTCCAATATGACTGACCAGAACACGAATGAGTACTTGGAGAAGATCAAACAGCGACTGTTTGAGAACCTGAGGATGCTGC
CACATGCACCCGGGGTCCAAATGCAGGCGATTCCTGAGGACGCCATCCCTGAGGAGAGTGGCGATGAAGACGAAGAAGAC
CCTGACAAGCACATCTCGATCTGCTCCTCTGACAAACGAATTGCCTGTCAGGAAGAGTTCTCAGACTGAAGAGGAGGGAG
AGGGGGGCCGCAAGAACGCTTCCAACTTCAAAAAAGCCAAGAGAGTCAAAACAGAGGATGAACAAGAGAAAGAGCCAGAG
GAGAAGAAAGAAGTCACAGAAAAGGAGAAAACCAAGGAGGAGAAGCCAGAAGCCAAAGGGGTCAAAGAGGAGGTCAAGTT
GGCC

Alignment

ORF - retro_cjac_2490 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 95.24 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MAQTQGTRRKVCYYYDGDVGNYYYGQGHPMKPHRIRMTHNLLLNYGLYRKMEIYRPHKANAEEMTKYHSD
          MAQ.QGT.RKVCYYYDGDVGNYYYGQGHPMKPHRIRMTHNLLLNYGLY.KMEIYRPHKANAEEMTKYHSD
Retrocopy MAQMQGTWRKVCYYYDGDVGNYYYGQGHPMKPHRIRMTHNLLLNYGLYQKMEIYRPHKANAEEMTKYHSD

Parental  DYIKFLRSIRPDNMSEYSKQMQRFNVGEDCPVFDGLFEFCQLSTGGSVASAVKLNKQQTDIAVNWAGGLH
          DYIKFLRSIRPDNMSEYSKQMQRFNVGEDCPVFDGLFEFC.LSTGGSVASAVKLNKQQ.DIAVNWAGGLH
Retrocopy DYIKFLRSIRPDNMSEYSKQMQRFNVGEDCPVFDGLFEFC*LSTGGSVASAVKLNKQQMDIAVNWAGGLH

Parental  HAKKSEASGFCYVNDIVLAILELLKYHQRVLYIDIDIHHGDGVEEAFYTTDRVMTVSFHKYGEYFPGTGD
          HAKK.EASGFCYVND.VLAILELLKYHQRVLYIDIDIHHGDGVEEAFYTTDRVMTVSFHKYGEYFPGTGD
Retrocopy HAKKFEASGFCYVNDTVLAILELLKYHQRVLYIDIDIHHGDGVEEAFYTTDRVMTVSFHKYGEYFPGTGD

Parental  LRDIGAGKGKYYAVNYPLRDGIDDESYEAIFKPVMSKVMEMFQPSAVVLQCGSDSLSGDRLGCFNLTIKG
          LRDIGAGKGKYYA.N.PL.DGID.ESYEAIFKPVMSKVMEMFQPSAVVLQCGSDSLSGDRLGCFNLTI.G
Retrocopy LRDIGAGKGKYYAINCPLQDGIDNESYEAIFKPVMSKVMEMFQPSAVVLQCGSDSLSGDRLGCFNLTITG

Parental  HAKCVEFVKSFNLPMLMLGGGGYTIRNVARCWTYETAVALDTEIPNELPYNDYFEYFGPDFKLHISPSNM
          HAKCVEFVKSFNLPMLMLGGGGYTIRNVA.CWTYETAVALDTE.PNELPYNDYFEYFGPDFKLHISPSNM
Retrocopy HAKCVEFVKSFNLPMLMLGGGGYTIRNVAQCWTYETAVALDTEMPNELPYNDYFEYFGPDFKLHISPSNM

Parental  TNQNTNEYLEKIKQRLFENLRMLPHAPGVQMQAIPEDAIPEESGDEDEEDPDKRISICSSDKRIACEEEF
          T.QNTNEYLEKIKQRLFENLRMLPHAPGVQMQAIPEDAIPEESGDEDEEDPDK.ISICSSDKRIAC.EEF
Retrocopy TDQNTNEYLEKIKQRLFENLRMLPHAPGVQMQAIPEDAIPEESGDEDEEDPDKHISICSSDKRIACQEEF

Parental  SD-SEEEGEGGRKNSSNFKKAKRVKTEDEKEKEPEEKKEVTEEEKTKEEKPEAKGVKEEVKLA
          SD..EE.GEGGRKN.SNFKKAKRVKTEDE.EKEPEEKKEVTE.EKTKEEKPEAKGVKEEVKLA
Retrocopy SD>EEE-GEGGRKNASNFKKAKRVKTEDEQEKEPEEKKEVTEKEKTKEEKPEAKGVKEEVKLA

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	0.87 RPM	31.55 RPM
SRP051959_heart	0.61 RPM	12.61 RPM
SRP051959_kidney	0.82 RPM	22.72 RPM
SRP051959_liver	0.37 RPM	11.91 RPM
SRP051959_lung	0.72 RPM	25.56 RPM
SRP051959_lymph_node	0.82 RPM	39.47 RPM
SRP051959_skeletal_muscle	0.33 RPM	6.31 RPM
SRP051959_spleen	1.20 RPM	27.08 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_2490 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_2490 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_2490 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 12 parental genes, and 16 retrocopies.

Species	Parental gene accession	Retrocopies number
Ciona intestinalis	ENSCING00000002649	1 retrocopy	retro_cint_18,
Callithrix jacchus	ENSCJAG00000000970	2 retrocopies	retro_cjac_2490 , retro_cjac_830,
Homo sapiens	ENSG00000116478	1 retrocopy	retro_hsap_826,
Gorilla gorilla	ENSGGOG00000011741	1 retrocopy	retro_ggor_676,
Myotis lucifugus	ENSMLUG00000013837	1 retrocopy	retro_mluc_283,
Macaca mulatta	ENSMMUG00000009948	2 retrocopies	retro_mmul_1085, retro_mmul_2518,
Mus musculus	ENSMUSG00000028800	1 retrocopy	retro_mmus_153,
Nomascus leucogenys	ENSNLEG00000002473	1 retrocopy	retro_nleu_259,
Pelodiscus sinensis	ENSPSIG00000004134	1 retrocopy	retro_psin_44,
Pteropus vampyrus	ENSPVAG00000013325	1 retrocopy	retro_pvam_1339,
Rattus norvegicus	ENSRNOG00000009568	3 retrocopies	retro_rnor_1091, retro_rnor_1098, retro_rnor_2457,
Sarcophilus harrisii	ENSSHAG00000008787	1 retrocopy	retro_shar_573,