RetrogeneDB ID: retro_cjac_2398

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 4:197308..197653(-)
• Located in intron of: ENSCJAG00000012363

Retrocopy information

• Ensembl ID: ENSCJAG00000012383
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: TAF12
• Ensembl ID: ENSCJAG00000009742
• Aliases: None
• Description: TAF12 RNA polymerase II, TATA box binding protein (TBP)-associated factor, 20kDa [Source:HGNC Symbol;Acc:11545]

Sequence

>retro_cjac_2398
GGACAGGAAGTTAGCCCTGAAAACAATCAGGTATTGACCAAGAAGAAACTGCAGGCCTTAGTAAGAGAAGTGGATCCTAA
TGAGCAGTTGGATGAAGATGAGGAGGAGACGCTGCTGCAGATTGCTGATGATTTTATCGAGAGTGCGGTGACGGCCGCCT
GTCAGCTAGCACGGCGTTGCAAGTCCAGCACTCTGGAGGTGAAAGACGCCCAGCTACATTCAGAGCGCCAGCGGAACACG
TGCATCCCAGGATTTGGCTCTGAAGAAATCCGACCCTACAAAAAAGCTTGCACCACGGAAGCTCACAAACGGAGAATGGC
ATTGATCCGGAAAACAACACACAGA

Alignment

ORF - retro_cjac_2398 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 85.22 %
• Parental protein coverage: 71.43 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  GGRLSPENNQVLTKKKLQDLVREVDPNEQLDEDVEEMLLQIADDFIESVVTAACQLARHRKSSTLEVKDV
          G...SPENNQVLTKKKLQ.LVREVDPNEQLDED.EE.LLQIADDFIES.VTAACQLAR..KSSTLEVKD.
Retrocopy GQEVSPENNQVLTKKKLQALVREVDPNEQLDEDEEETLLQIADDFIESAVTAACQLARRCKSSTLEVKDA

Parental  QLHLERQWNMWIPGFGSEEIRPYKKACTTEAHKQRMALIRKTTKK
          QLH.ERQ.N..IPGFGSEEIRPYKKACTTEAHK.RMALIRKTT..
Retrocopy QLHSERQRNTCIPGFGSEEIRPYKKACTTEAHKRRMALIRKTTHR

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	0.69 RPM	5.64 RPM
SRP051959_heart	0.21 RPM	6.00 RPM
SRP051959_kidney	0.29 RPM	6.15 RPM
SRP051959_liver	0.13 RPM	7.32 RPM
SRP051959_lung	0.42 RPM	10.05 RPM
SRP051959_lymph_node	0.80 RPM	10.16 RPM
SRP051959_skeletal_muscle	0.09 RPM	8.43 RPM
SRP051959_spleen	0.55 RPM	11.72 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_2398 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_2398 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_2398 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 16 parental genes, and 36 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000004366	4 retrocopies	retro_chof_1112, retro_chof_2145, retro_chof_2182, retro_chof_402,
Callithrix jacchus	ENSCJAG00000009742	1 retrocopy	retro_cjac_2398 ,
Cavia porcellus	ENSCPOG00000009044	3 retrocopies	retro_cpor_1211, retro_cpor_352, retro_cpor_895,
Dipodomys ordii	ENSDORG00000015036	1 retrocopy	retro_dord_384,
Echinops telfairi	ENSETEG00000012597	2 retrocopies	retro_etel_129, retro_etel_540,
Macropus eugenii	ENSMEUG00000000914	3 retrocopies	retro_meug_1305, retro_meug_1609, retro_meug_1730,
Myotis lucifugus	ENSMLUG00000012595	8 retrocopies	retro_mluc_1214, retro_mluc_2541, retro_mluc_2542, retro_mluc_2598, retro_mluc_403, retro_mluc_412, retro_mluc_415, retro_mluc_416,
Monodelphis domestica	ENSMODG00000010943	1 retrocopy	retro_mdom_603,
Mustela putorius furo	ENSMPUG00000015506	1 retrocopy	retro_mputfur_458,
Oryctolagus cuniculus	ENSOCUG00000003935	2 retrocopies	retro_ocun_510, retro_ocun_712,
Ochotona princeps	ENSOPRG00000001524	1 retrocopy	retro_opri_503,
Rattus norvegicus	ENSRNOG00000048288	1 retrocopy	retro_rnor_2638,
Sorex araneus	ENSSARG00000007568	5 retrocopies	retro_sara_243, retro_sara_35, retro_sara_358, retro_sara_441, retro_sara_570,
Tarsius syrichta	ENSTSYG00000005320	1 retrocopy	retro_tsyr_1288,
Tursiops truncatus	ENSTTRG00000005548	1 retrocopy	retro_ttru_1943,
Vicugna pacos	ENSVPAG00000006779	1 retrocopy	retro_vpac_362,