RetrogeneDB ID: retro_cjac_4218

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: X:117221495..117222173(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSCJAG00000032679
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: ZCCHC17
• Ensembl ID: ENSCJAG00000006259
• Aliases: None
• Description: zinc finger, CCHC domain containing 17 [Source:HGNC Symbol;Acc:30246]

Sequence

>retro_cjac_4218
ATGAATTCAGGAAGGCCCGAGACCATGGAAAAATTGCCTGCTCTCTACACTATTTTCCATGGAGAGGTTGCTATGGTGAC
AGACTATGGAGCCTTTATCAAAATCCCAGGCTGTCGGAAACAAGGTCTGGTCCATCGAACTCATATGTCATCCTGTCGGG
TGGATAAGCCCTCTGAGATAGTAGATGTCGGAGACAAAGTATGGGTGAAGCTTATTGGCCGAGAGATGAAAAATGATAGG
ATAACAGTATCCCTCTCCATGAAAGTTGTCAACCAAGGGACTGGGAAAGACCTTGATCCCAACAACATTATCATTGAGCA
AGAAGAGAGGCGGAGGCGGTCCTTCCAGGATTACACTGGGCAGAAGATCACCCTTGAGGCTGTTTTGAACACTACTTGCA
AGAAGTGTGGCTGTAAAGGCCACTTTGCAAAAGATTGTTTCATGCAACCAGGTGGGACTAAATATTCTCTGATACCTGAT
GAGGAAGAGGAAAAGGAAGAGCCAAAGTCAGCAGAGTTTGAGAAGCCCAACCCCACAAGGAATTCTTCTAGAAAAAGAAA
GAAGGAGAAGAAGAAAAAGAAACATAGAGACAGGAAGTCGTCTGTTTCTGACAGCTCAGACTCTGAGAGTGAAACAGGCA
AGAGGGCAAGGCACACATCAAAAGACAGCAAGGCAGCA

Alignment

ORF - retro_cjac_4218 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 98.23 %
• Parental protein coverage: 93.78 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MNSGRPETMENLPALYTIFQGEVAMVTDYGAFIKIPGCRKQGLVHRTHMSSCRVDKPSEIVDVGDKVWVK
          MNSGRPETME.LPALYTIF.GEVAMVTDYGAFIKIPGCRKQGLVHRTHMSSCRVDKPSEIVDVGDKVWVK
Retrocopy MNSGRPETMEKLPALYTIFHGEVAMVTDYGAFIKIPGCRKQGLVHRTHMSSCRVDKPSEIVDVGDKVWVK

Parental  LIGREMKNDRIKVSLSMKVVNQGTGKDLDPNNIIIEQEERRRRSFQDYTGQKITLEAVLNTTCKKCGCKG
          LIGREMKNDRI.VSLSMKVVNQGTGKDLDPNNIIIEQEERRRRSFQDYTGQKITLEAVLNTTCKKCGCKG
Retrocopy LIGREMKNDRITVSLSMKVVNQGTGKDLDPNNIIIEQEERRRRSFQDYTGQKITLEAVLNTTCKKCGCKG

Parental  HFAKDCFMQPGGTKYSLIPDEEEEKEEPKSAEFEKPNPTRNSSRKRKKEKKKKKHRDRKSSDSDSSDSES
          HFAKDCFMQPGGTKYSLIPDEEEEKEEPKSAEFEKPNPTRNSSRKRKKEKKKKKHRDRKSS.SDSSDSES
Retrocopy HFAKDCFMQPGGTKYSLIPDEEEEKEEPKSAEFEKPNPTRNSSRKRKKEKKKKKHRDRKSSVSDSSDSES

Parental  ETGKRARHTSKDSKAA
          ETGKRARHTSKDSKAA
Retrocopy ETGKRARHTSKDSKAA

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	0.27 RPM	10.94 RPM
SRP051959_heart	0.26 RPM	9.58 RPM
SRP051959_kidney	0.11 RPM	9.41 RPM
SRP051959_liver	0.28 RPM	6.32 RPM
SRP051959_lung	0.34 RPM	10.44 RPM
SRP051959_lymph_node	0.25 RPM	10.23 RPM
SRP051959_skeletal_muscle	0.20 RPM	6.81 RPM
SRP051959_spleen	0.23 RPM	11.43 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_4218 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_4218 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_4218 has 0 orthologous retrocopies within eutheria group .

---

Parental genes homology:

Parental genes homology involve 12 parental genes, and 15 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000017710	1 retrocopy	retro_amel_1501,
Bos taurus	ENSBTAG00000016818	2 retrocopies	retro_btau_168, retro_btau_273,
Canis familiaris	ENSCAFG00000011131	2 retrocopies	retro_cfam_485, retro_cfam_835,
Callithrix jacchus	ENSCJAG00000006259	1 retrocopy	retro_cjac_4218 ,
Dipodomys ordii	ENSDORG00000004128	1 retrocopy	retro_dord_200,
Echinops telfairi	ENSETEG00000007421	1 retrocopy	retro_etel_1280,
Loxodonta africana	ENSLAFG00000015364	1 retrocopy	retro_lafr_534,
Monodelphis domestica	ENSMODG00000017082	1 retrocopy	retro_mdom_252,
Mus musculus	ENSMUSG00000028772	1 retrocopy	retro_mmus_2150,
Otolemur garnettii	ENSOGAG00000013749	1 retrocopy	retro_ogar_1225,
Ictidomys tridecemlineatus	ENSSTOG00000003825	1 retrocopy	retro_itri_405,
Tursiops truncatus	ENSTTRG00000014870	2 retrocopies	retro_ttru_1383, retro_ttru_1613,