RetrogeneDB ID: retro_cjac_4127

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: X:125079696..125080451(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSCJAG00000013800
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: PNO1
• Ensembl ID: ENSCJAG00000006564
• Aliases: None
• Description: RNA-binding protein PNO1 [Source:RefSeq peptide;Acc:NP_001257650]

Sequence

>retro_cjac_4127
TTGGACTCCGAAATGGAAGCACAGAGCGCCAGGGCTGAGGAGGGCTTTACCCAGGTCACCCGCAAGGGTGGCCAGCGGGC
GAAAAAACGGCAGGCTGAACAGCTGTCCGCAGAGGGAGAGGGCGGGGATGCGGGCCTTACGGACGCAGAAGAGGCCAGGC
CGGCGAAGAGGCCCGTCTTCTCGCCCCTCTGCGGTGACGGGCTCCTGAGTGGGAAAGAAGAAACAAGGAAAATTCCAGTC
CCAGCTAACAGGTACACACCATTAAAAGAAAACTGGATGAAGATATTTACTCCTATTGTGGAACATTTGGGACTTCAGAT
AAGCTTTAATTTGAAATCAAGGAATGTAGAAATCAGGACTTGTAAAGAAACCGGGGATGTTAGTGCTCTGGCAAAAGCAG
CTGATTTTGTGAAAGCCTTATTCTCGGCTTTCAGGTGGAGGATGCACTTGCCCTCCTCAGGTTGGATGGCCTCTTCCTAG
AGTCTTTTGAAATTACAGATGTTAAACCCTTAAAGGGAGACCACCTATCCAGGGCAATAGGAAGAATTGCTGGCGAAGGA
GGAAAAACCAAATTCAACATAGAGAATGTGACACGGACGCGGATAGTTTTGGCTGATGTGAAAGTTTACATCCTTGTCTC
CTTCCAAAACATCAAGATGGCAAGAACTGCCATTTGCAACCTAATCTTGGGAAATCCTCCTTCCAAGGTTTATGGCAATA
TTCGAGCTGTGGCTAGCAGATCAGCAGATAGATTC

Alignment

ORF - retro_cjac_4127 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 92.49 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  LESEMEAQSAGAEDGFTQVTRKGGRRAKKRQAEQLSAAGEGGDAGLMDTEEARPAKRPVFPPLCGDGLLS
          L.SEMEAQSA.AE.GFTQVTRKGG.RAKKRQAEQLSA.GEGGDAGL.D.EEARPAKRPVF.PLCGDGLLS
Retrocopy LDSEMEAQSARAEEGFTQVTRKGGQRAKKRQAEQLSAEGEGGDAGLTDAEEARPAKRPVFSPLCGDGLLS

Parental  GKEETRKIPVPANRYTPLKENWMKIFTPIVEHLGLQIRFNLKSRNVEIRTCKETRDVSALTKAADFVKA-
          GKEETRKIPVPANRYTPLKENWMKIFTPIVEHLGLQI.FNLKSRNVEIRTCKET.DVSAL.KAADFVKA.
Retrocopy GKEETRKIPVPANRYTPLKENWMKIFTPIVEHLGLQISFNLKSRNVEIRTCKETGDVSALAKAADFVKA<

Parental  FILGFQVEDALALIRLDDLFLESFEITDVKPLKGDHLSRAIGRIAGKGGKTKFTIENVTRTRIVLADVKV
          .ILGFQVEDALAL.RLD.LFLESFEITDVKPLKGDHLSRAIGRIAG.GGKTKF.IENVTRTRIVLADVKV
Retrocopy LILGFQVEDALALLRLDGLFLESFEITDVKPLKGDHLSRAIGRIAGEGGKTKFNIENVTRTRIVLADVKV

Parental  HILGSFQNIKMARTAICNLILGNPPSKVYGNIRAVASRSADRF
          .IL.SFQNIKMARTAICNLILGNPPSKVYGNIRAVASRSADRF
Retrocopy YILVSFQNIKMARTAICNLILGNPPSKVYGNIRAVASRSADRF

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	8.30 RPM
SRP051959_heart	0.00 RPM	6.54 RPM
SRP051959_kidney	0.04 RPM	11.60 RPM
SRP051959_liver	0.02 RPM	8.86 RPM
SRP051959_lung	0.02 RPM	5.81 RPM
SRP051959_lymph_node	0.00 RPM	6.96 RPM
SRP051959_skeletal_muscle	0.00 RPM	8.87 RPM
SRP051959_spleen	0.00 RPM	7.52 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_4127 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_4127 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_4127 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 14 parental genes, and 19 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000003256	1 retrocopy	retro_cfam_1886,
Callithrix jacchus	ENSCJAG00000006564	3 retrocopies	retro_cjac_2615, retro_cjac_273, retro_cjac_4127 ,
Felis catus	ENSFCAG00000025330	2 retrocopies	retro_fcat_1521, retro_fcat_864,
Loxodonta africana	ENSLAFG00000000046	1 retrocopy	retro_lafr_419,
Microcebus murinus	ENSMICG00000010897	1 retrocopy	retro_mmur_516,
Myotis lucifugus	ENSMLUG00000010850	1 retrocopy	retro_mluc_1719,
Macaca mulatta	ENSMMUG00000017461	2 retrocopies	retro_mmul_102, retro_mmul_352,
Nomascus leucogenys	ENSNLEG00000009993	1 retrocopy	retro_nleu_2389,
Oryctolagus cuniculus	ENSOCUG00000006100	1 retrocopy	retro_ocun_47,
Otolemur garnettii	ENSOGAG00000016637	1 retrocopy	retro_ogar_3025,
Pongo abelii	ENSPPYG00000012353	1 retrocopy	retro_pabe_1232,
Rattus norvegicus	ENSRNOG00000005524	1 retrocopy	retro_rnor_712,
Sus scrofa	ENSSSCG00000008352	2 retrocopies	retro_sscr_114, retro_sscr_352,
Tarsius syrichta	ENSTSYG00000004007	1 retrocopy	retro_tsyr_1625,