RetrogeneDB ID: retro_cjac_2437

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 4:48854170..48855034(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSCJAG00000011899
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSCJAG00000036548
• Aliases: None
• Description: None

Sequence

>retro_cjac_2437
TTCTGTAAAACGTGTATTGTTTGTTACCTGGAGACCAGCAAGTACTGTCCTATTTGTGACGTCCAAGTTCTCAAAATCAG
ACCACTACTGAATATAAGGTCAGATAAATCTCTTCAAGATAGCCTATACAAATTAGTTCCAGGACTTTTCAAAAAGGAAA
TGAAGAGAACAAGGGATTTTTATGCAGCTCATCCTTCCGCTGAAGCTGCCAATGGTTCTAATGAAGACAGAGGAGAGGTT
GCAGATGAAGATAAGAGAATTATAACTGATGATGAGATAATGAGCTTATCCATTGAATTCTTTGACCAGAACAGATTGGA
TCGGAAAGTAAACAAAGACAAAGAGAAATCTAAGGAGGAGCTGAATGATAAAAGATATTTACGAAACCCAGCAGCAATGA
CTGTGATGCACTTACATAAGTTTCTCAGAGGTAAAATGGACATACCTAATACTTTCCAGATTGATGTCATGTATAAGGAG
GAACCTTTAAAGGGTTATTATACACTAATGGAAATTGCCTACATTTATACCTAGAGAAGGAATGGTCCACTTTCTTTGAA
ACACAGAGTTCGACCTACTTGTAAAAGAATGAAGATCAGTCACCAGAGAGATGGACTGACAAATGCTGGAGAACTGGAAA
GTGACTCTGGGAGTGAAGAGGCCAACAGCCCAGCAGGAGGTATTCCCTCCACCTCTTCTTGTTTGCCTAGCCCCAGTACT
TCAGTGCAGTCTCCCCATCCACACTTTCCTCACATTTCCAGTACTATGAATGGAACCAGTAACAGCCCCAGCGGTAACCA
CTAATCTTTTGCCAACAGACCTTGAAAATCATCAGTAAATGGGTCATCAGCAACTTCTTCTGGT

Alignment

ORF - retro_cjac_2437 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 90.31 %
• Parental protein coverage: 88.65 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  FCKTCIVRYLETSKYCPICDVQVHKTRPLLNIRSDKTLQDIVYKLVPGLFKNEMKRRRDFYAAHPSADAA
          FCKTCIV.YLETSKYCPICDVQV.K.RPLLNIRSDK.LQD..YKLVPGLFK.EMKR.RDFYAAHPSA.AA
Retrocopy FCKTCIVCYLETSKYCPICDVQVLKIRPLLNIRSDKSLQDSLYKLVPGLFKKEMKRTRDFYAAHPSAEAA

Parental  NGSNEDRGEVADEDKRIITDDEIISLSIEFFDQNRLDRKVNKDKEKSKEEVNDKRYLRCPAAMTVMHLRK
          NGSNEDRGEVADEDKRIITDDEI.SLSIEFFDQNRLDRKVNKDKEKSKEE.NDKRYLR.PAAMTVMHL.K
Retrocopy NGSNEDRGEVADEDKRIITDDEIMSLSIEFFDQNRLDRKVNKDKEKSKEELNDKRYLRNPAAMTVMHLHK

Parental  FLRSKMDIPNTFQIDVMYEEEPLKDYYTLMDIAYIYTWRRNGPLPLKYRVRPTCKRMKISHQRDGLTNAG
          FLR.KMDIPNTFQIDVMY.EEPLK.YYTLM.IAYIYT.RRNGPL.LK.RVRPTCKRMKISHQRDGLTNAG
Retrocopy FLRGKMDIPNTFQIDVMYKEEPLKGYYTLMEIAYIYT*RRNGPLSLKHRVRPTCKRMKISHQRDGLTNAG

Parental  ELESDSGSDKANSPAGGIPSTSSCLPSPSTPVQSPHPQFPHISSTMNGTSNSPSGNHQSSFASRPRKSSV
          ELESDSGS..ANSPAGGIPSTSSCLPSPST.VQSPHP.FPHISSTMNGTSNSPSGNH..SFA.RP.KSSV
Retrocopy ELESDSGSEEANSPAGGIPSTSSCLPSPSTSVQSPHPHFPHISSTMNGTSNSPSGNH-*SFANRP*KSSV

Parental  NGSSATSSG
          NGSSATSSG
Retrocopy NGSSATSSG

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	0.07 RPM	7.65 RPM
SRP051959_heart	0.19 RPM	15.54 RPM
SRP051959_kidney	0.18 RPM	13.13 RPM
SRP051959_liver	0.15 RPM	8.19 RPM
SRP051959_lung	0.13 RPM	13.47 RPM
SRP051959_lymph_node	0.14 RPM	16.85 RPM
SRP051959_skeletal_muscle	0.04 RPM	9.28 RPM
SRP051959_spleen	0.23 RPM	21.91 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_2437 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_2437 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_2437 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

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

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000011962	1 retrocopy	retro_chof_709,
Callithrix jacchus	ENSCJAG00000001960	1 retrocopy	retro_cjac_707,
Callithrix jacchus	ENSCJAG00000011001	1 retrocopy	retro_cjac_2702,
Callithrix jacchus	ENSCJAG00000036548	1 retrocopy	retro_cjac_2437 ,
Cavia porcellus	ENSCPOG00000015427	2 retrocopies	retro_cpor_1209, retro_cpor_546,
Gorilla gorilla	ENSGGOG00000025243	1 retrocopy	retro_ggor_3025,
Loxodonta africana	ENSLAFG00000016845	1 retrocopy	retro_lafr_591,
Macaca mulatta	ENSMMUG00000000881	1 retrocopy	retro_mmul_2591,
Mus musculus	ENSMUSG00000026739	1 retrocopy	retro_mmus_3710,
Oryctolagus cuniculus	ENSOCUG00000005420	1 retrocopy	retro_ocun_489,
Tupaia belangeri	ENSTBEG00000015631	1 retrocopy	retro_tbel_2369,