RetrogeneDB ID: retro_cjac_3342

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: ACFV01158669.1:17247..18115(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: RBM22
• Ensembl ID: ENSCJAG00000020963
• Aliases: None
• Description: None

Sequence

>retro_cjac_3342
CAGACATGCCTCTTAGACCTGGAGCATGGCCTGCCTATCCAGGTTTGTGATACAGAATTGTCTTTATAAGATGACATGCC
AAAGTCAGATGTCAGAGAAGAGTACTACATGCAGAATGTGGAGAGAGGGGTTTCTAACTCAGATTGAAGATGGCCAGTTG
GCCTGCTGGGGAAAGCCACATCCACCAGTGACATGCTGGACAAACTGGCCAGACCATACCCTATTACCTAAGGAATAAGC
CCCACATTTTCTCCTTTTGGGGGAAGGGAGAGGGTAAGAGAGGAGAGGAGTTTCCATACAGACATGAGAAGCCTACAGGT
CCACATGATTCCCTTGCTGATCAGATATTAAAGATCAATATTATGGAGTCAATGACCCTGTAGCAGATACGCTTTGATAG
TAGGTTTCAACCACACCTCATCTGGAACTACCAGAGGACAAGTCTATCCCCATACTAGATGTTAGTGGTCTGGGTGATAC
CATTACCGAGACAGATCTTAAGAAATAATCTCTACCTCTTTAGAGAGATCTGGACAATCCCTATTGTGCAGAGACAATGG
TGTGCTTTCATCCAGGTTTCCACAGGGCAGGCTGCACAAGTGGCAGCAGAGAAGTCCTTTAATAAGTTAACCGTCAATGG
CTGCAGACTCAGTGTAAAATGGGAAGATCCCAGGCAGCCAGAGGAAAGGAAAATGACAGAACCCCAGACCCTGGGATCCA
GCTAGAGCCAATTCCAGCACTGATGGAAGCAATTCCTCCTGCAGCAGCAGCAGATGCATCTGCCAATGACTTCAAGCAAC
CCCCGAGTGCTCCTTCAGCTGTGGTGTGTATTGCCTGGCCATGTTCAATGGCTATTGCCCTGCCCCCA

Alignment

ORF - retro_cjac_3342 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 68.9 %
• Parental protein coverage: 70.07 %
• Number of stop codons detected: 5
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  QTCLLDLEYAGLPIQVRDAGLSFKDDMPKSDVNKEYYTQNMEREISNSDGTRPVGMLGKATSTSDMLLKL
          QTCLLDLE..GLPIQV.D..LS..DDMPKSDV..EYY.QN.ER..SNSD...PVG.LGKATSTSDML.KL
Retrocopy QTCLLDLEH-GLPIQVCDTELSL*DDMPKSDVREEYYMQNVERGVSNSD*RWPVGLLGKATSTSDMLDKL

Parental  AR-TTPYYKRNRPHICSFWVKGECKRGEECPYRHEKPTDPDDPLADQ-NIKDRYYGINDPVADKLLKRAS
          AR.T.PYY.RN.PHI.SFW.KGE.KRGEE.PYRHEKPT.P.D.LADQ..IKD.YYG.NDPVAD.L....S
Retrocopy AR<TIPYYLRNKPHIFSFWGKGEGKRGEEFPYRHEKPTGPHDSLADQ<DIKDQYYGVNDPVADTL***VS

Parental  TMPRLDPPEDKTITTLYVGGLGDTITETD-LRNHFYQFGEIRTITVVQRQQCAFIQFATRQAAEVAAEKS
          T.P.L..PEDK.I..L.V.GLGDTITETD.LRN..Y.F.EI.TI..VQRQ.CAFIQ..T.QAA.VAAEKS
Retrocopy TTPHLELPEDKSIPILDVSGLGDTITETD>LRNNLYLFREIWTIPIVQRQWCAFIQVSTGQAAQVAAEKS

Parental  FNKLIVNGRRLNVKW-GRSQAARGKEKEKDGTTDSGIKLEPVPGLPGALPPPPAAEEEASANYFNLPPSG
          FNKL.VNG.RL.VKW.GRSQAARG..KE.D.T.D.GI.LEP.P.L..A...PPAA...ASAN.F..PPS.
Retrocopy FNKLTVNGCRLSVKW<GRSQAARG--KENDRTPDPGIQLEPIPALMEAI--PPAAAADASANDFKQPPSA

Parental  PPAVVNIALPPPPGIAPPP
          P.AVV.IA.P....IA.PP
Retrocopy PSAVVCIAWPCSMAIALPP

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	0.00 RPM	5.95 RPM
SRP051959_heart	0.00 RPM	5.68 RPM
SRP051959_kidney	0.00 RPM	7.10 RPM
SRP051959_liver	0.00 RPM	5.33 RPM
SRP051959_lung	0.00 RPM	9.08 RPM
SRP051959_lymph_node	0.00 RPM	11.03 RPM
SRP051959_skeletal_muscle	0.00 RPM	8.23 RPM
SRP051959_spleen	0.00 RPM	9.05 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_3342 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_3342 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_3342 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 13 parental genes, and 31 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000018082	1 retrocopy	retro_cfam_1480,
Callithrix jacchus	ENSCJAG00000020963	6 retrocopies	retro_cjac_1338, retro_cjac_2471, retro_cjac_3342 , retro_cjac_3390, retro_cjac_3934, retro_cjac_990,
Cavia porcellus	ENSCPOG00000001946	2 retrocopies	retro_cpor_280, retro_cpor_283,
Dasypus novemcinctus	ENSDNOG00000011166	1 retrocopy	retro_dnov_2298,
Homo sapiens	ENSG00000086589	2 retrocopies	retro_hsap_3465, retro_hsap_4273,
Gorilla gorilla	ENSGGOG00000012947	2 retrocopies	retro_ggor_2337, retro_ggor_2859,
Myotis lucifugus	ENSMLUG00000009040	2 retrocopies	retro_mluc_1453, retro_mluc_153,
Macaca mulatta	ENSMMUG00000020683	4 retrocopies	retro_mmul_1199, retro_mmul_1348, retro_mmul_1553, retro_mmul_1762,
Monodelphis domestica	ENSMODG00000009574	1 retrocopy	retro_mdom_186,
Otolemur garnettii	ENSOGAG00000011086	1 retrocopy	retro_ogar_2206,
Pongo abelii	ENSPPYG00000015955	4 retrocopies	retro_pabe_1412, retro_pabe_1594, retro_pabe_2861, retro_pabe_3486,
Pan troglodytes	ENSPTRG00000017423	2 retrocopies	retro_ptro_2348, retro_ptro_2898,
Tarsius syrichta	ENSTSYG00000003939	3 retrocopies	retro_tsyr_1090, retro_tsyr_1187, retro_tsyr_1231,