RetrogeneDB ID: retro_cjac_3829

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: GL284860.1:22349..22821(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: SDHD
• Ensembl ID: ENSCJAG00000010975
• Aliases: None
• Description: succinate dehydrogenase complex, subunit D, integral membrane protein [Source:HGNC Symbol;Acc:10683]

Sequence

>retro_cjac_3829
ATGGCGGTTCTCTGGAGACTTAGTGCTCTTTGCCGTGCCCAAGGAAGCCGAGCTCTGTTGCTGCGAACTTCAGTGGTCAG
ACCTGCTCATATTTCAGCGTTTCTTCAGGACCAACCTACCCCAGAATGGTGTGGAGTGCACCACATTCACTTGTCACCGA
GTCACCATTCTGGTTCCAAGGCTGCATCTCTCCACTGGACTAGTGAAAGGGTTGTCAGTGTTTTGCTCCTGGGTCTGCTT
CCGGCTGCTTATTTGAATCCTTGCTCTGCGATGGACTATTCTCTGGCTGCAACTCTCACTCTTCATGGTCACTGGGGCCT
TGGACAAGTTGTTACTATGTTCATGGGGATGCCTCGCAGAAAGCTGCCAAGGCAGGGCTTTTGGCACTTTCAGCTTTAAC
CTTTGCTGGGCTTTGCTATTTCACTATCACGATGTGGGCATCTGCAAAGCTGTTGCCATGCTATGGAAGCTC

Alignment

ORF - retro_cjac_3829 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 86.96 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  MAVLWRLSALCCAQGGRALLLRTSVVRPAHISAFLQNQPTPEWCGMQHIHLSPSHHSGSKTASLHWTSER
          MAVLWRLSALC.AQG.RALLLRTSVVRPAHISAFLQ.QPTPEWCG..HIHLSPSHHSGSK.ASLHWTSER
Retrocopy MAVLWRLSALCRAQGSRALLLRTSVVRPAHISAFLQDQPTPEWCGVHHIHLSPSHHSGSKAASLHWTSER

Parental  VVSVLLLGLLPAAYLNPCSAMDYSLAATLTLHGHWGLGQVVTDYVHGDASQKAAKAG-LLALSALTFAGL
          VVSVLLLGLLPAAYLNPCSAMDYSLAATLTLHGHWGLGQVVT....G....K....G.LLALSALTFAGL
Retrocopy VVSVLLLGLLPAAYLNPCSAMDYSLAATLTLHGHWGLGQVVTMFM-GMPRRKLPRQG<LLALSALTFAGL

Parental  CY-FNYHDVGICKAVAMLWKL
          CY.F.YHDVGICKAVAMLWKL
Retrocopy CY<FHYHDVGICKAVAMLWKL

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	0.24 RPM	14.27 RPM
SRP051959_heart	0.44 RPM	24.66 RPM
SRP051959_kidney	0.82 RPM	28.04 RPM
SRP051959_liver	0.71 RPM	33.01 RPM
SRP051959_lung	0.39 RPM	7.89 RPM
SRP051959_lymph_node	0.23 RPM	6.42 RPM
SRP051959_skeletal_muscle	0.70 RPM	46.32 RPM
SRP051959_spleen	0.11 RPM	13.19 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_3829 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_3829 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_3829 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 8 parental genes, and 26 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000010975	4 retrocopies	retro_cjac_1385, retro_cjac_1390, retro_cjac_1557, retro_cjac_3829 ,
Echinops telfairi	ENSETEG00000008424	1 retrocopy	retro_etel_252,
Homo sapiens	ENSG00000204370	8 retrocopies	retro_hsap_124, retro_hsap_1912, retro_hsap_2132, retro_hsap_2182, retro_hsap_2729, retro_hsap_2784, retro_hsap_355, retro_hsap_3791,
Gorilla gorilla	ENSGGOG00000026496	1 retrocopy	retro_ggor_50,
Loxodonta africana	ENSLAFG00000002763	1 retrocopy	retro_lafr_432,
Macaca mulatta	ENSMMUG00000015247	1 retrocopy	retro_mmul_224,
Otolemur garnettii	ENSOGAG00000008568	5 retrocopies	retro_ogar_1651, retro_ogar_1795, retro_ogar_2087, retro_ogar_3122, retro_ogar_3147,
Pongo abelii	ENSPPYG00000003876	5 retrocopies	retro_pabe_1549, retro_pabe_1924, retro_pabe_2233, retro_pabe_2999, retro_pabe_3096,