RetrogeneDB ID: retro_cjac_3290

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 9:35890190..35891019(-)
• Located in intron of: ENSCJAG00000008072

Retrocopy information

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

Parental gene information

• Parental gene symbol: ADIPOR2
• Ensembl ID: ENSCJAG00000000683
• Aliases: None
• Description: adiponectin receptor 2 [Source:HGNC Symbol;Acc:24041]

Sequence

>retro_cjac_3290
ATGAACGAGCCAACAGAAAACCGATTGGGGTGCAGCAGGACTCCAGAGCCAGATATAAGGCTCAGAAAAGGGCACCAACT
TGACGGTACAAGGAGAGGTGATAATGACAGCCACCAAGGAGATTTAGAGCCCATGTTAGAGGCATCTGTTGTATCTTCCC
ATGATAAAGCTCTGAGAATCACGAGTGCAGTGATGAAGGTCCGCAGGAAGATGAGGGGTTTATGGGCATGTGCCCTCTCT
TACAAGCCCATCATGCTATGAAAAAATAGAAGAATGTGTTTGTAAGGTATGGGAAGGTCAGTGGGGAGTGATTTCTCATG
ATGTATTACCAGACTGGCTCAAGGATAACGACTTTCTTTTACATGGACACCGACCTCCTGTGCCTTCTTTCCAGGCCTGT
TTTAAGAGCATTTTCAGAATACACACAGAAACAGGCAACATCTGGACACATCTCTTAGTTTGTGTATTCTTCTTGTGCCT
GGGGATCTTTTATACGTTTTGCCCAAGTATCTCCTTTGTGGCCCCTCTGCAAGAGAAGGTGGTCTTTGGATTATTTTTCT
TAGGAGCCATTCTCTGCCTTTCTTTTTTATGGCTCTTCCATACAGTCTACTGCCACTCAGAGGGGGTCTCCCAGATCTTC
TCTAAACTGGATTACTCTGATATTGCTCTTCTGATTATGGGAAGTTTTGTTCCTTGGCTTTATTATTCTTTCTACTGTAA
TCCACAACCTTGCTTCATCTACTTGATTGTCATCTGTGTGCTGGGCATTGCAGCCATTATAGTCTCCCAGTGGGACATGT
TTGCTACCCCTCAGTATTCTGGGCCTAGG

Alignment

ORF - retro_cjac_3290 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 90.36 %
• Parental protein coverage: 72.02 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  MNEPTENRLGCSRTPEPDIRLRKGHQLDGTRRGDNDSHQGYLEPMLEASVVSSHDKK-SSEEHECSDEAP
          MNEPTENRLGCSRTPEPDIRLRKGHQLDGTRRGDNDSHQG.LEPMLEAS.V.S...K.SSE.HECSDE.P
Retrocopy MNEPTENRLGCSRTPEPDIRLRKGHQLDGTRRGDNDSHQGDLEPMLEAS-VVSSHDK<SSENHECSDEGP

Parental  QEDEGFMGMSPLLQAHHAM-EKMEEFVCKVWEGRWRVIPHDVLPDWLKDNDFLLHGHRPPMPSFRACFKS
          QEDEGFMGM.PLLQAHHAM.EK.EE.VCKVWEG.W.VI.HDVLPDWLKDNDFLLHGHRPP.PSF.ACFKS
Retrocopy QEDEGFMGMCPLLQAHHAM<EKIEECVCKVWEGQWGVISHDVLPDWLKDNDFLLHGHRPPVPSFQACFKS

Parental  IFRIHTETGNIWTHLLGCVFFLCLGIFYMFRPNISFVAPLQEKVVFGLFFLGAILCLSFSWLFHTVYCHS
          IFRIHTETGNIWTHLL.CVFFLCLGIFY.F.P.ISFVAPLQEKVVFGLFFLGAILCLSF.WLFHTVYCHS
Retrocopy IFRIHTETGNIWTHLLVCVFFLCLGIFYTFCPSISFVAPLQEKVVFGLFFLGAILCLSFLWLFHTVYCHS

Parental  EGVSRIFSKLDYSGIALLIMGSFVPWLYYSFYCNPQPCFIYLIVICVLGIAAIIVSQWDMFATPQYRGVR
          EGVS.IFSKLDYS.IALLIMGSFVPWLYYSFYCNPQPCFIYLIVICVLGIAAIIVSQWDMFATPQY.G.R
Retrocopy EGVSQIFSKLDYSDIALLIMGSFVPWLYYSFYCNPQPCFIYLIVICVLGIAAIIVSQWDMFATPQYSGPR

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	0.53 RPM	15.18 RPM
SRP051959_heart	1.84 RPM	18.43 RPM
SRP051959_kidney	1.62 RPM	19.19 RPM
SRP051959_liver	1.06 RPM	21.86 RPM
SRP051959_lung	0.62 RPM	16.80 RPM
SRP051959_lymph_node	0.96 RPM	12.81 RPM
SRP051959_skeletal_muscle	0.70 RPM	21.75 RPM
SRP051959_spleen	0.90 RPM	14.79 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_3290 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_3290 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_3290 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 6 parental genes, and 10 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000009050	1 retrocopy	retro_btau_320,
Callithrix jacchus	ENSCJAG00000000683	3 retrocopies	retro_cjac_2912, retro_cjac_3290 , retro_cjac_504,
Callithrix jacchus	ENSCJAG00000006268	3 retrocopies	retro_cjac_2262, retro_cjac_740, retro_cjac_741,
Loxodonta africana	ENSLAFG00000021355	1 retrocopy	retro_lafr_249,
Microcebus murinus	ENSMICG00000005653	1 retrocopy	retro_mmur_818,
Myotis lucifugus	ENSMLUG00000002211	1 retrocopy	retro_mluc_66,