RetrogeneDB ID: retro_psin_44

Retrocopy location

• Organism: Chinese softshell turtle (Pelodiscus sinensis)
• Coordinates: JH208240.1:1353582..1354317(+)
• Located in intron of: ENSPSIG00000015473

Retrocopy information

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

Parental gene information

• Parental gene symbol: HDAC1
• Ensembl ID: ENSPSIG00000004134
• Aliases: None
• Description: histone deacetylase 1 [Source:HGNC Symbol;Acc:4852]

Sequence

>retro_psin_44
ATGGTGCTGACATAGGGGACCAAGTAGAAAGTCTGTTACTACTATGATGGGGATGTTGCAAACTACTATTATGGCTAGGG
CCATCCAACAAAACCCCACAGGATACAAATGACCCACAACCTCCTGCCAAACTATAGTCTCTACAGAAAAACGGCACCAC
ATCAACCCCACAAGACAAACGTAGAAGAAATGACCAAGTATCATGGTGATGATTACATTACATTTCTGAGATCTATTCAC
CCTGATAACTTGTCTGAGTACAGCAGGCAGATGCAGAGATTCAATGTTGGGAAAGATTGCCCAGTGTCTGAATGGTTGTT
TGAGTTTTGTCAGCTGTCTGCAGGAGGTTCTGTAGCCAGCACTGTGAAGCTGAACAAGCAACAGACAGATATTGCTGTGA
ATTGGGCAGGAGGCCTTCACCATGCTAAGAAATAGAAGGCTTCTGGCTTCTGTTACGTCAGTGACATTGTCTTAGCCATC
TTAGAGCTCCTAAAGTACAACCAGAGGGTGCTGTATATTGACACTGATATTCATCATGGCAATGGCATGGAGGAAGCCTT
TTACACCACAGACTGTGTCATGACTGCCTCCTTTCATAAGTACAGCGAATACTTCCCAGGAGCAGGGGATCTGTGGGATA
TCGGTGCAGGTAAAAGCAAGTATTATGCCGTCAACTATCCTACCTGGGACAGAATTGACGATGAGTCCTATGCAGCAATA
TGTAAGCCGGTAATA

Alignment

ORF - retro_psin_44 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 80.82 %
• Parental protein coverage: 50.11 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MALTQGTKRKVCYYYDGDVGNYYYGQGHPMKPHRIRMTHNLL-QMEIYR---PH---KANAEEMTKYHSD
          M.LT.GTK.KVCYYYDGDV.NYYYG.GHP.KPHRI.MTHNLL.....YR...PH...K.N.EEMTKYH.D
Retrocopy MVLT*GTK*KVCYYYDGDVANYYYG*GHPTKPHRIQMTHNLLPNYSLYRKTAPHQPHKTNVEEMTKYHGD

Parental  DYIKFLRSIRPDNMSEYSKQMQRFNVGEDCPVFDGLFEFCQLSAGGSVASAVKLNKQQTDIAVNWAGGLH
          DYI.FLRSI.PDN.SEYS.QMQRFNVG.DCPV...LFEFCQLSAGGSVAS.VKLNKQQTDIAVNWAGGLH
Retrocopy DYITFLRSIHPDNLSEYSRQMQRFNVGKDCPVSEWLFEFCQLSAGGSVASTVKLNKQQTDIAVNWAGGLH

Parental  HAKKSEASGFCYVNDIVLAILELLKYHQRVLYIDIDIHHGDGVEEAFYTTDRVMTASFHKYGEYFPGTGD
          HAKK..ASGFCYV.DIVLAILELLKY.QRVLYID.DIHHG.G.EEAFYTTD.VMTASFHKY.EYFPG.GD
Retrocopy HAKK*KASGFCYVSDIVLAILELLKYNQRVLYIDTDIHHGNGMEEAFYTTDCVMTASFHKYSEYFPGAGD

Parental  LRDIGAGKGKYYAVNYPLRDGIDDESYEAIFKPVI
          L.DIGAGK.KYYAVNYP..D.IDDESY.AI.KPVI
Retrocopy LWDIGAGKSKYYAVNYPTWDRIDDESYAAICKPVI

Legend:

• *: Stop codon
• >: Forward frameshift by one nucleotide
• <: Reverse frameshift by one nucleotide

Expression

RNA-Seq

Pelodiscus sinensis was not studied using RNA-Seq expression data.

ChIP-Seq

Pelodiscus sinensis was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_psin_44 retrocopy.

TSS

Pelodiscus sinensis was not studied using FANTOM5 data.

Lab

retro_psin_44 was not experimentally validated.

Homology

Retrocopy orthology:

Pelodiscus sinensis does not belong to any of the species groups (eutheria, teleost or neognath), studied for retrocopy-based homology. For more information about studied groups, please go to help section.

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Parental genes homology:

Parental genes homology involve 14 parental genes, and 20 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,
Otolemur garnettii	ENSOGAG00000005709	3 retrocopies	retro_ogar_2181, retro_ogar_3022, retro_ogar_3313,
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,
Tursiops truncatus	ENSTTRG00000001613	1 retrocopy	retro_ttru_1236,