RetrogeneDB ID: retro_cjac_1289

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 14:62929337..62929771(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: KRTCAP2
• Ensembl ID: ENSCJAG00000009017
• Aliases: None
• Description: keratinocyte associated protein 2 [Source:HGNC Symbol;Acc:28942]

Sequence

>retro_cjac_1289
TTGGCCAGAGGCTCCAATTTGACTCAAGGGTGCGGCATGATGGTGGTGGGTATAGGCACCTCACTAGCAATCTCCTCCCT
CCTGTCCCTGCTGCTCTTCGCTCGGATGCAGATGTACAGCTGTCAGCTGGCATCCACTGAGTGGCTTACCATTCAGGGAG
CACTGCTTGGCTCAGGTCTCCTCGTGTTCTTCCTCACTGCATTCAAGGTTCTGGAGAATCTTATCTTTGGCAAAGGATCC
CAAGTAAAGATCTTCTCTGAGATTCTCCTGTACCTCCTGTTGGCTGTCTTTGCATCTAGCCTCATCCACTGAGTCTGTTT
CATCTTCTCCATGGTTGGTCTGTACTACATCAATAAGACCTCCTCCACTCTGTACCCACCAGCAGCTCCATTCCTCACAC
CAGCCAAGGTCACAGGAAGAGCAAGAGGAGAAAT

Alignment

ORF - retro_cjac_1289 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 78.0 %
• Parental protein coverage: 91.98 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  LARGADWTHRRGMMVVGTGTSLALSSLLSLLLFAGMQMYSRQLASTEWLTIQGGLLGSGLFVFSLTAFNN
          LARG...T...GMMVVG.GTSLA.SSLLSLLLFA.MQMYS.QLASTEWLTIQG.LLGSGL.VF.LTAF..
Retrocopy LARGSNLTQGCGMMVVGIGTSLAISSLLSLLLFARMQMYSCQLASTEWLTIQGALLGSGLLVFFLTAFKV

Parental  LENLVFGKGFQAKIFPEILLCLLLALFASGLIHRVCVTTCFIFSMVGLYYINKISSTLYQAAAPVLTPAK
          LENL.FGKG.Q.KIF.EILL.LLLA.FAS.LIH.VC....FIFSMVGLYYINK.SSTLY..AAP.LTPAK
Retrocopy LENLIFGKGSQVKIFSEILLYLLLAVFASSLIH*VC----FIFSMVGLYYINKTSSTLYPPAAPFLTPAK

Parental  VTG-KSKKRN
          VTG.KSK.RN
Retrocopy VTG<KSKRRN

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	6.43 RPM
SRP051959_heart	0.00 RPM	5.75 RPM
SRP051959_kidney	0.00 RPM	8.12 RPM
SRP051959_liver	0.00 RPM	7.56 RPM
SRP051959_lung	0.00 RPM	7.13 RPM
SRP051959_lymph_node	0.00 RPM	6.80 RPM
SRP051959_skeletal_muscle	0.00 RPM	8.56 RPM
SRP051959_spleen	0.00 RPM	7.39 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_1289 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_1289 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_1289 has 5 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_2100
Pan troglodytes	retro_ptro_1541
Gorilla gorilla	retro_ggor_1635
Pongo abelii	retro_pabe_1999
Macaca mulatta	retro_mmul_987

---

Parental genes homology:

Parental genes homology involve 16 parental genes, and 20 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000011336	1 retrocopy	retro_amel_1789,
Canis familiaris	ENSCAFG00000017055	1 retrocopy	retro_cfam_1487,
Callithrix jacchus	ENSCJAG00000009017	1 retrocopy	retro_cjac_1289 ,
Felis catus	ENSFCAG00000025085	3 retrocopies	retro_fcat_1496, retro_fcat_477, retro_fcat_576,
Homo sapiens	ENSG00000163463	1 retrocopy	retro_hsap_2100,
Gorilla gorilla	ENSGGOG00000009303	1 retrocopy	retro_ggor_1635,
Macaca mulatta	ENSMMUG00000012180	2 retrocopies	retro_mmul_745, retro_mmul_987,
Mustela putorius furo	ENSMPUG00000005647	1 retrocopy	retro_mputfur_1653,
Nomascus leucogenys	ENSNLEG00000011864	1 retrocopy	retro_nleu_1306,
Oryctolagus cuniculus	ENSOCUG00000000347	1 retrocopy	retro_ocun_157,
Otolemur garnettii	ENSOGAG00000030271	1 retrocopy	retro_ogar_1306,
Pongo abelii	ENSPPYG00000000756	1 retrocopy	retro_pabe_1999,
Pan troglodytes	ENSPTRG00000001410	1 retrocopy	retro_ptro_1541,
Rattus norvegicus	ENSRNOG00000020542	1 retrocopy	retro_rnor_2128,
Ictidomys tridecemlineatus	ENSSTOG00000008829	1 retrocopy	retro_itri_1127,
Tarsius syrichta	ENSTSYG00000013228	2 retrocopies	retro_tsyr_1096, retro_tsyr_531,