RetrogeneDB ID: retro_cjac_2464

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 4:110855728..110856517(-)
• Located in intron of: ENSCJAG00000005204

Retrocopy information

• Ensembl ID: ENSCJAG00000005207
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: APOOL
• Ensembl ID: ENSCJAG00000008249
• Aliases: None
• Description: apolipoprotein O-like [Source:HGNC Symbol;Acc:24009]

Sequence

>retro_cjac_2464
ATGGGAAAACTGACAACCATGCTGGCAGGTCTGATTTATGCATCTGTAAGTGTACATGCAACCAAAGAAGAGGAATCCAA
AAAGCAGCTAGTGAAACCAGAGCAGCTCCCCATGTATACTGCACCACCGCTCCAGTCTAAACATGTTGAAGAGCAGCCTG
GTCATTTACAAATGAGCTTTGCTTCCATCCACACTGCAACTGGTCGTTATATTGGCTGGTGCAAGGGTGTTTATGTCTTT
GCAAAAAATGGGATAATGGATACAGTACAATTTGGAAAAGATGACTATGTCTATCTGAAGAATCCTCCTCAAGATATTCT
TCTGAAAATGGGAGTTATTATAGTTTCAGGATTGGTGGGCTTGGTTTCAGAGAGAAAAGGTTCTAAGTTTAAGAAAATTA
CTTATCCTCTGGGACTGGCCACTTTAGGAGCAACTGTTTGCTACCCAATTCAGTCAGTAATAATTGCTAAGGTAACAGGG
AAAAAGATATATGCTACAAGCCAGCAAATTTTTGAAACAATTAAATCGCTGTGGACAAAAAGCAACAAAAAAGAGTCACT
TCGTCAACCTAAGGAAAAAACTAAGCTAGGATCCTCTGCCGAAACAGAAGTATCTGCAAAAACAACTCACGTCTTGAAAC
ACTCAGTGCCTTTGCCAACAGAACTCAGCTCTGAAGCAAAGACCAAATCAGTATCCACCTCAGGTGCTACACCGTTTATG
CCTGACCCCAACCTCATGGATCACAGGCAGTCCCATCCAGAAGATACAGATATGTACAGCACTAGAAGC

Alignment

ORF - retro_cjac_2464 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 89.35 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MGKLTTMPAGLIYASVSVHSTKEEESKKQLVKPEQLPIYTAPPLQSKYVEEQPGHLQMGFASIRTATGRY
          MGKLTTM.AGLIYASVSVH.TKEEESKKQLVKPEQLP.YTAPPLQSK.VEEQPGHLQM.FASI.TATGRY
Retrocopy MGKLTTMLAGLIYASVSVHATKEEESKKQLVKPEQLPMYTAPPLQSKHVEEQPGHLQMSFASIHTATGRY

Parental  IGWCKGVYVFVKNGITNTVQFGKDAYVYLKSPPQDFLPKMGVITVSGLVGLVSARKGSKFKKITYPLGLA
          IGWCKGVYVF.KNGI..TVQFGKD.YVYLK.PPQD.L.KMGVI.VSGLVGLVS.RKGSKFKKITYPLGLA
Retrocopy IGWCKGVYVFAKNGIMDTVQFGKDDYVYLKNPPQDILLKMGVIIVSGLVGLVSERKGSKFKKITYPLGLA

Parental  TLGATVCYPVQSVIITKVTGKKIYATSQQTFETVKSLWTKSNKKESLPQPKEKTKLGSSAEIEAFAKTTH
          TLGATVCYP.QSVII.KVTGKKIYATSQQ.FET.KSLWTKSNKKESL.QPKEKTKLGSSAE.E..AKTTH
Retrocopy TLGATVCYPIQSVIIAKVTGKKIYATSQQIFETIKSLWTKSNKKESLRQPKEKTKLGSSAETEVSAKTTH

Parental  VLKHSVPLPAELSSEAKTKSVSTSGATQFMPDPKLMDHGQSHPEDIDMYSTRS
          VLKHSVPLP.ELSSEAKTKSVSTSGAT.FMPDP.LMDH.QSHPED.DMYSTRS
Retrocopy VLKHSVPLPTELSSEAKTKSVSTSGATPFMPDPNLMDHRQSHPEDTDMYSTRS

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	0.24 RPM	7.01 RPM
SRP051959_heart	0.47 RPM	9.70 RPM
SRP051959_kidney	2.13 RPM	9.21 RPM
SRP051959_liver	0.11 RPM	12.13 RPM
SRP051959_lung	0.07 RPM	5.50 RPM
SRP051959_lymph_node	0.14 RPM	3.65 RPM
SRP051959_skeletal_muscle	2.88 RPM	9.22 RPM
SRP051959_spleen	0.57 RPM	5.40 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_2464 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_2464 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_2464 has 0 orthologous retrocopies within eutheria group .

---

Parental genes homology:

Parental genes homology involve 19 parental genes, and 33 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000000829	1 retrocopy	retro_amel_1035,
Canis familiaris	ENSCAFG00000017383	1 retrocopy	retro_cfam_1490,
Callithrix jacchus	ENSCJAG00000004909	8 retrocopies	retro_cjac_1360, retro_cjac_1417, retro_cjac_1448, retro_cjac_1767, retro_cjac_1792, retro_cjac_1896, retro_cjac_2038, retro_cjac_2063,
Callithrix jacchus	ENSCJAG00000008249	2 retrocopies	retro_cjac_1783, retro_cjac_2464 ,
Dipodomys ordii	ENSDORG00000011045	1 retrocopy	retro_dord_373,
Equus caballus	ENSECAG00000009229	1 retrocopy	retro_ecab_577,
Homo sapiens	ENSG00000155008	1 retrocopy	retro_hsap_3253,
Gorilla gorilla	ENSGGOG00000016329	1 retrocopy	retro_ggor_2213,
Loxodonta africana	ENSLAFG00000008844	1 retrocopy	retro_lafr_1035,
Microcebus murinus	ENSMICG00000015844	1 retrocopy	retro_mmur_1511,
Myotis lucifugus	ENSMLUG00000011384	1 retrocopy	retro_mluc_1364,
Macaca mulatta	ENSMMUG00000004335	1 retrocopy	retro_mmul_2045,
Mustela putorius furo	ENSMPUG00000001899	3 retrocopies	retro_mputfur_606, retro_mputfur_734, retro_mputfur_874,
Nomascus leucogenys	ENSNLEG00000002634	1 retrocopy	retro_nleu_1702,
Pongo abelii	ENSPPYG00000020516	1 retrocopy	retro_pabe_2697,
Pan troglodytes	ENSPTRG00000022067	1 retrocopy	retro_ptro_2200,
Sus scrofa	ENSSSCG00000012459	1 retrocopy	retro_sscr_610,
Tupaia belangeri	ENSTBEG00000010147	5 retrocopies	retro_tbel_2037, retro_tbel_2609, retro_tbel_2840, retro_tbel_3361, retro_tbel_3737,
Tursiops truncatus	ENSTTRG00000000429	1 retrocopy	retro_ttru_1337,