RetrogeneDB ID: retro_cjac_2957

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 7:149192652..149193084(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSCJAG00000031803
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: ZFAND2A
• Ensembl ID: ENSCJAG00000015776
• Aliases: None
• Description: zinc finger, AN1-type domain 2A [Source:HGNC Symbol;Acc:28073]

Sequence

>retro_cjac_2957
ATGGAGTTTCCTGATTTGGGGAAGTATTGTTCAGAAAAAACTTGCAAGCAGTTAGATTTTCTTCCAGTAAAATGTGATAC
ATGTAAACAAGATTTCTGTAAAGATCATTTTACATATGCTGCACATAAGCGTCCATTTGCATTCCAGAAGGATGTTCAAG
TCCCGGTGTGCCCACTCTGTAATATCCCCATCCCAATAACAAAGGGACAGATCCCAGCCGTGGTGGCTGGCGATCATATG
GATGGAGACTGTGACTGTCATCCTGGGAAGAAGAAAGAGATTTTTACATACCGGCGCTCAAAAGAGGGCTGCAAGAAGAA
AGAGATGCTGCAGATGGTGTGTGCCCAGTGTCATGGCAACTTCTGCATCCAGCACAGACATCCCCTGGACCACAGCTGCA
GACACAGGAGCCGCCCCACTATCAAAGCTGGG

Alignment

ORF - retro_cjac_2957 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 90.34 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MEFPDLGKHCSEKTCKQLDFLPVKCDMCKQDFCKDHFTYAAHKCPCAFQKDVQVPVCPLCNIPIPIKKGQ
          MEFPDLGK.CSEKTCKQLDFLPVKCD.CKQDFCKDHFTYAAHK.P.AFQKDVQVPVCPLCNIPIPI.KGQ
Retrocopy MEFPDLGKYCSEKTCKQLDFLPVKCDTCKQDFCKDHFTYAAHKRPFAFQKDVQVPVCPLCNIPIPITKGQ

Parental  VPDVVVGDHMDRDCGYHPGKKKEKIFTYRCSKEGCKKKEMLQMVCAQCHGNFCIQHRHPLDHSCTHRSRP
          .P.VV.GDHMD.DC..HPGKKKE.IFTYR.SKEGCKKKEMLQMVCAQCHGNFCIQHRHPLDHSC.HRSRP
Retrocopy IPAVVAGDHMDGDCDCHPGKKKE-IFTYRRSKEGCKKKEMLQMVCAQCHGNFCIQHRHPLDHSCRHRSRP

Parental  TIKAG
          TIKAG
Retrocopy TIKAG

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	0.09 RPM	3.06 RPM
SRP051959_heart	0.00 RPM	2.77 RPM
SRP051959_kidney	0.07 RPM	3.57 RPM
SRP051959_liver	0.00 RPM	7.47 RPM
SRP051959_lung	0.73 RPM	4.54 RPM
SRP051959_lymph_node	0.00 RPM	3.13 RPM
SRP051959_skeletal_muscle	0.00 RPM	2.88 RPM
SRP051959_spleen	0.00 RPM	4.20 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_2957 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_2957 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_2957 has 0 orthologous retrocopies within eutheria group .

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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	ENSCJAG00000015776	1 retrocopy	retro_cjac_2957 ,
Loxodonta africana	ENSLAFG00000005496	1 retrocopy	retro_lafr_211,
Microcebus murinus	ENSMICG00000002112	1 retrocopy	retro_mmur_441,
Monodelphis domestica	ENSMODG00000025494	1 retrocopy	retro_mdom_34,
Sarcophilus harrisii	ENSSHAG00000000364	2 retrocopies	retro_shar_756, retro_shar_779,
Tupaia belangeri	ENSTBEG00000007079	2 retrocopies	retro_tbel_2636, retro_tbel_2697,