RetrogeneDB ID: retro_cjac_2331

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 4:40152003..40152549(+)
• Located in intron of: ENSCJAG00000005885

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSCJAG00000008211
• Aliases: None
• Description: None

Sequence

>retro_cjac_2331
TGCACCAATGGCCACGTGAAAGTGATCACTCTCCTGGTAAACTGAAAATGCCAGATTGACCTTGGTGACAAATGAAACAA
TATGACTTTGATGAAGGCTGTACATTGTCAAAAAGAGACCTGTGTCATCATTCTGTTAGAACGTGGCACCAATCTAGATC
TTCCAGATGTCTACGGCAACATTGCTCTCTACTATACTGTCTATAATGAGAATAGACTACTGGCAGAAAAACTCTCTTCA
CACCATGTGAATACTGAAGTGCCAGAACAAGGATGGAAACACACTGCTTTTACTTGTTGTAGTTTGCAAAACACAGTAAA
AGGTGGAATTTTAGTGAAGAAACAGGCAAATATATATGCTGTTGATAGGTTGAAAAGAACAGCCCTCATACCTATTGTAC
ATTATAGCTTGTCAGGTATAGTTAGCATTCTTCTTCAACAAAATATTGTCTTTACTCAAGAATATGTATGAACACACAGC
CCATGTTTACACTATTTCTGGTGGTCTGACAAGCACTCACAACAAATTTTGCAAAATTTGCAAAAA

Alignment

ORF - retro_cjac_2331 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 50.8 %
• Parental protein coverage: 69.06 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  CAHGRVEVVTLLVSRNCRIDIDDRLNRTPLMKAVHGQEEACSIILLEHGANPNIQDVFGNTALHYAVYNS
          C..G.V.V.TLLV...C.ID..D..N...LMKAVH.Q.E.C.IILLE.G.N....DV.GN.AL.Y.VYN.
Retrocopy CTNGHVKVITLLVN*KCQIDLGDK*NNMTLMKAVHCQKETCVIILLERGTNLDLPDVYGNIALYYTVYNE

Parental  VTSLAEKLLSYHANTE-AINKEGNTPLLLAVICKRQKMVKF-LVKNQANVHAVDNFNRTALMLASYHDFP
          ...LAEKL.S.H.NTE...NK.GNT.LLL.V.CK.Q..V.F.LVK.QAN..AVD...RTAL.........
Retrocopy NRLLAEKLSSHHVNTE>CQNKDGNTLLLLVVVCKTQ*KVEF<LVKKQANIYAVDRLKRTALIPIVHYSLS

Parental  SIVSLLLKENVSIFSQD-MFGQTAEDYAVYCGLL-RIQQQILEHKNK
          .IVS.LL..N...F.Q..M...TA..Y....GL.....QQIL....K
Retrocopy GIVSILLQQNI-VFTQE>MYEHTAHVYTISGGLT<KHSQQILQNLQK

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	0.29 RPM	0.16 RPM
SRP051959_heart	0.32 RPM	1.28 RPM
SRP051959_kidney	0.27 RPM	0.38 RPM
SRP051959_liver	0.24 RPM	0.26 RPM
SRP051959_lung	0.42 RPM	0.21 RPM
SRP051959_lymph_node	0.80 RPM	0.07 RPM
SRP051959_skeletal_muscle	0.04 RPM	0.17 RPM
SRP051959_spleen	0.40 RPM	0.82 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_2331 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_2331 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_2331 has 1 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Macaca mulatta	retro_mmul_1761

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Parental genes homology:

Parental genes homology involve 6 parental genes, and 8 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000008211	2 retrocopies	retro_cjac_2331 , retro_cjac_2672,
Microcebus murinus	ENSMICG00000017899	2 retrocopies	retro_mmur_1151, retro_mmur_246,
Macaca mulatta	ENSMMUG00000008983	1 retrocopy	retro_mmul_1761,
Nomascus leucogenys	ENSNLEG00000016858	1 retrocopy	retro_nleu_2713,
Pongo abelii	ENSPPYG00000019046	1 retrocopy	retro_pabe_1037,
Tupaia belangeri	ENSTBEG00000017150	1 retrocopy	retro_tbel_490,