RetrogeneDB ID: retro_cjac_4198

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: X:84812693..84813659(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSCJAG00000001728
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: RNF2
• Ensembl ID: ENSCJAG00000005442
• Aliases: None
• Description: ring finger protein 2 [Source:HGNC Symbol;Acc:10061]

Sequence

>retro_cjac_4198
AAAACATGGGAACTCAGTTTATATGAATTACAACGAACACCTCAGGAGGCAATAACAGATGCTTTAGAAATTGTGGTGTC
ACGTCGAAGTCTACACAGTGAATCTATGTGCCCAATTTGTTTGGATACGTTGAAGAATACTATGAATGACTACAAAGGAG
TGCATCGTTTTTGTGCAGACTGCATCATCACAGCCCTTAGAAGTGGCAACAAAGAATGTCCCACCTGTCGGAAAAAAACT
AGTTTCCAAAAAATCACTAAGGCCAGACCCGAACTTTGATACACTCATCAGCAAAATTTATCCACGTCATGATGAGTATG
AAGCTCATCAAGAGAGAGTATTAGCCAGTATCAACAAGCACGATAATCAGCAAGCACTCAGTCACAGCATTGGGGAAGGA
CTGATGATACAGGGCATGAATAGACTGCAGCGAGGCAAGAAACAACAGATTGAAAATGGCAGTGGAGCAGAAGATAATGG
TGACAGTTCACACTGTAGTAATGCCTCCACACACAGCAATCAGGAAGCAGGCCCTAGTAACAACGGACCAAAATATCTGA
TGATTCTGAGCTTGATATTGATCATAACAATGCAGCAGTGGCAATTGATCCAGTAATGGATGGTGCTGGTGAAACTGAAT
TAGTATTCAGGCCTCACCCTGCCCTTACGGACAAAGATGAGAGTATACAGACAAGGTACATAAAGACTTCAGATAACGCC
ACTGTTGATCACTTATCCAAGTATCTGACTGTGAGGTTAGCTTTAGAAGAACTTCAAAGCAAAGGTGAATCAAACCAGTT
GAACCTTGATACAGCCAGTGAGAAGCACTATACCATTTATATGGCAACAGCCAGTGACCAGTTCACTATATTAAATGGCT
CTTTTTCTTTTGAATTGGTGAGTGAGAAATACTGGAAAGTGAACAAACCTATGGAACTTTACCACGCACCTACAAAGGAG
CACAAA

Alignment

ORF - retro_cjac_4198 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 86.42 %
• Parental protein coverage: 95.83 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  KTWELSLYELQRTPQEAITDGLEIVVSPRSLHSELMCPICLDMLKNTMTTKECLHRFCADCIITALRSGN
          KTWELSLYELQRTPQEAITD.LEIVVS.RSLHSE.MCPICLD.LKNTM......HRFCADCIITALRSGN
Retrocopy KTWELSLYELQRTPQEAITDALEIVVSRRSLHSESMCPICLDTLKNTMNDYKGVHRFCADCIITALRSGN

Parental  KECPTCRKK-LVSKRSLRPDPNFDALISKIYPSRDEYEAHQERVLARINKHNNQQALSHSIEEGLKIQAM
          KECPTCRKK.LVSK.SLRPDPNFD.LISKIYP..DEYEAHQERVLA.INKH.NQQALSHSI.EGL.IQ.M
Retrocopy KECPTCRKK>LVSKKSLRPDPNFDTLISKIYPRHDEYEAHQERVLASINKHDNQQALSHSIGEGLMIQGM

Parental  NRLQRGKKQQIENGSGAEDNGDSSHCSNASTHSNQEAGPSN-KRTKTSDDSGLELDNNNAAVAIDPVMDG
          NRLQRGKKQQIENGSGAEDNGDSSHCSNASTHSNQEAGPSN..RTK.SDDS.L..D.NNAAVAIDPVMDG
Retrocopy NRLQRGKKQQIENGSGAEDNGDSSHCSNASTHSNQEAGPSN<QRTKISDDSELDIDHNNAAVAIDPVMDG

Parental  ASEIELVFRPHPTLMEKDDSAQTRYIKTSGNATVDHLSKYLAVRLALEELRSKGESNQMNLDTASEKQYT
          A.E.ELVFRPHP.L..KD.S.QTRYIKTS.NATVDHLSKYL.VRLALEEL.SKGESNQ.NLDTASEK.YT
Retrocopy AGETELVFRPHPALTDKDESIQTRYIKTSDNATVDHLSKYLTVRLALEELQSKGESNQLNLDTASEKHYT

Parental  IYIATASGQFTVLNGSFSLELVSEKYWKVNKPMELYYAPTKEHK
          IY.ATAS.QFT.LNGSFS.ELVSEKYWKVNKPMELY.APTKEHK
Retrocopy IYMATASDQFTILNGSFSFELVSEKYWKVNKPMELYHAPTKEHK

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	7.06 RPM
SRP051959_heart	0.00 RPM	15.30 RPM
SRP051959_kidney	0.02 RPM	14.13 RPM
SRP051959_liver	0.00 RPM	6.87 RPM
SRP051959_lung	0.00 RPM	13.40 RPM
SRP051959_lymph_node	0.00 RPM	13.88 RPM
SRP051959_skeletal_muscle	0.00 RPM	6.11 RPM
SRP051959_spleen	0.00 RPM	14.18 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_4198 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_4198 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_4198 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 17 parental genes, and 33 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000011199	3 retrocopies	retro_chof_1450, retro_chof_2217, retro_chof_2251,
Callithrix jacchus	ENSCJAG00000005442	1 retrocopy	retro_cjac_4198 ,
Erinaceus europaeus	ENSEEUG00000014091	1 retrocopy	retro_eeur_88,
Echinops telfairi	ENSETEG00000015824	1 retrocopy	retro_etel_2081,
Felis catus	ENSFCAG00000009609	1 retrocopy	retro_fcat_1725,
Homo sapiens	ENSG00000121481	2 retrocopies	retro_hsap_4056, retro_hsap_4226,
Gorilla gorilla	ENSGGOG00000014400	1 retrocopy	retro_ggor_2724,
Loxodonta africana	ENSLAFG00000021357	1 retrocopy	retro_lafr_407,
Myotis lucifugus	ENSMLUG00000001129	1 retrocopy	retro_mluc_2187,
Monodelphis domestica	ENSMODG00000007422	1 retrocopy	retro_mdom_857,
Nomascus leucogenys	ENSNLEG00000018029	2 retrocopies	retro_nleu_1042, retro_nleu_554,
Oryctolagus cuniculus	ENSOCUG00000004892	1 retrocopy	retro_ocun_838,
Pongo abelii	ENSPPYG00000000417	2 retrocopies	retro_pabe_3331, retro_pabe_3374,
Pan troglodytes	ENSPTRG00000001775	2 retrocopies	retro_ptro_2749, retro_ptro_2871,
Ictidomys tridecemlineatus	ENSSTOG00000006625	3 retrocopies	retro_itri_1646, retro_itri_1794, retro_itri_410,
Tupaia belangeri	ENSTBEG00000016387	4 retrocopies	retro_tbel_1757, retro_tbel_3368, retro_tbel_3892, retro_tbel_4061,
Tarsius syrichta	ENSTSYG00000006109	6 retrocopies	retro_tsyr_1344, retro_tsyr_1647, retro_tsyr_2063, retro_tsyr_2083, retro_tsyr_227, retro_tsyr_474,