RetrogeneDB ID: retro_cjac_2988

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 7:70851669..70852400(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSCJAG00000001869
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: SDHB
• Ensembl ID: ENSCJAG00000007927
• Aliases: None
• Description: succinate dehydrogenase complex, subunit B, iron sulfur (Ip) [Source:HGNC Symbol;Acc:10681]

Sequence

>retro_cjac_2988
ATGGTGGCGGTGGTCGCACTGTCCTTGAGGCGCTGGTTCTCAGCCACAACCGTTGGTGGAGCCTGCCTGCAGGCCTGCCG
AGGAGCCCAGACAGCTGCAGCCCCAACTCCCCATATCAAGAAATTTGCCATCTATCGATGGGACCCAGACAAGGCTGGAG
ACAAACCTCATTTGCAGACTTATGAAGTTGACCTTAATAAATGTGGCCCCATGGTACTGGATGCCTTAATCAAGATTAAG
AATGAAATTGACTCTACTTTGACCTTCCGAAGATCATGCAGAGAAGGCATCTGTGGCTCTTGTGCAATGAACATCCATGG
AGGCAACACTCTAGCCTGCACCCGAAGGATTGATACCAACCTCAATAAAGTCTCAAAAATCTACCCTCTTCCGCATATGT
ATGTGATAAAGGATCTTGTTCCCGATTTGAGCAACTTCTATGCACAGCACAAATCCATTGAATCTTATTTAAAGAAGAAG
GATGAATCTCAGGGAGGCAAGCAGCAGTATCTGCAGTCCATAGAAGACTGTGAGAAACTGGATGGGCTCTATGAGTGCAT
TCTCTGTGCCTGTTGTAGCACCGGCTGCCCCAGCTACTGGTGGAACGGAGACAAATATCTGGGGCCTGCAGTTCTTATGC
AGGCCTGTGCTGGATGATTGACTCCAAAGACGACTTCACAGAGGAGCACCTGGCCAAGCTGCAGGACCCGTTCTCTCTGT
ACCGCTGCCAC

Alignment

ORF - retro_cjac_2988 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 93.06 %
• Parental protein coverage: 94.57 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MAAVVALSLRRRFPATTVGGACLQACRGAQTAAAAAPRIKKFAIYRWDPDKAGDKPHMQTYEVDLNKCGP
          M.AVVALSLRR.F.ATTVGGACLQACRGAQTAAA..P.IKKFAIYRWDPDKAGDKPH.QTYEVDLNKCGP
Retrocopy MVAVVALSLRRWFSATTVGGACLQACRGAQTAAAPTPHIKKFAIYRWDPDKAGDKPHLQTYEVDLNKCGP

Parental  MVLDALIKIKNEIDSTLTFRRSCREGICGSCAMNINGGNTLACTRRIDTNLNKVSKIYPLPHMYVIKDLV
          MVLDALIKIKNEIDSTLTFRRSCREGICGSCAMNI.GGNTLACTRRIDTNLNKVSKIYPLPHMYVIKDLV
Retrocopy MVLDALIKIKNEIDSTLTFRRSCREGICGSCAMNIHGGNTLACTRRIDTNLNKVSKIYPLPHMYVIKDLV

Parental  PDLSNFYAQYKSIEPYLKKKDESQGGKQQYLQSIEDREKLDGLYECILCACCSTSCPSYWWNGDKYLGPA
          PDLSNFYAQ.KSIE.YLKKKDESQGGKQQYLQSIED.EKLDGLYECILCACCST.CPSYWWNGDKYLGPA
Retrocopy PDLSNFYAQHKSIESYLKKKDESQGGKQQYLQSIEDCEKLDGLYECILCACCSTGCPSYWWNGDKYLGPA

Parental  VLMQAYR-WMIDSRDDFTEERLAKLQDPFSLYRCH
          VLMQA...WMIDS.DDFTEE.LAKLQDPFSLYRCH
Retrocopy VLMQACA<WMIDSKDDFTEEHLAKLQDPFSLYRCH

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	0.02 RPM	26.07 RPM
SRP051959_heart	0.02 RPM	60.67 RPM
SRP051959_kidney	0.02 RPM	66.11 RPM
SRP051959_liver	0.11 RPM	65.33 RPM
SRP051959_lung	0.00 RPM	18.87 RPM
SRP051959_lymph_node	0.02 RPM	17.40 RPM
SRP051959_skeletal_muscle	0.02 RPM	83.03 RPM
SRP051959_spleen	0.02 RPM	20.59 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_2988 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_2988 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_2988 has 0 orthologous retrocopies within eutheria group .

---

Parental genes homology:

Parental genes homology involve 11 parental genes, and 12 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000015832	1 retrocopy	retro_cfam_587,
Choloepus hoffmanni	ENSCHOG00000005664	1 retrocopy	retro_chof_2016,
Callithrix jacchus	ENSCJAG00000007927	1 retrocopy	retro_cjac_2988 ,
Loxodonta africana	ENSLAFG00000018475	1 retrocopy	retro_lafr_454,
Macropus eugenii	ENSMEUG00000004817	1 retrocopy	retro_meug_1106,
Microcebus murinus	ENSMICG00000016629	1 retrocopy	retro_mmur_1062,
Myotis lucifugus	ENSMLUG00000000032	1 retrocopy	retro_mluc_150,
Nomascus leucogenys	ENSNLEG00000013264	1 retrocopy	retro_nleu_1640,
Sorex araneus	ENSSARG00000013780	1 retrocopy	retro_sara_577,
Tupaia belangeri	ENSTBEG00000004803	2 retrocopies	retro_tbel_2480, retro_tbel_2875,
Xenopus tropicalis	ENSXETG00000013435	1 retrocopy	retro_xtro_60,