RetrogeneDB ID: retro_cjac_3224

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 9:60913974..60915075(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: PAIP1
• Ensembl ID: ENSCJAG00000001340
• Aliases: None
• Description: poly(A) binding protein interacting protein 1 [Source:HGNC Symbol;Acc:16945]

Sequence

>retro_cjac_3224
ATAGCTAAACCCCAGGTGGTTGTAGCATCTATATTAATGTCTACGCTGCCTGTGAATGCCCCTGAATTTTATCTTTCAGG
TTATTCTTCCAATTACACAGAATCCTATGGAGATGGTTGTTAGGATTATCCCACTCTATCTGAATATGTTCAGGATTTTT
TGGATCATCTTACAGAGCATCCTGGCAGTTTTGAAACTGAAATTGAACAGTTTGCCGAGACCCTGAATGGCTGGATTACA
ACAGATTATGCTTTGCAAGAACTTGTGGAACTCATATATCAACAGGACATGTCTATCCCGAATTTCTCTTATATAGGAGC
TTGCCTGTGTAATTACCTGTCCCATCATCTGACAATTAGCCCACAGAGTGGCAACTTCTGCCAGTTGCTACTTCAAAGAT
GTTGGACTGAATATGAAGTTAAAGATCAAGCTGCAAAAGGGGATGAAGTTACTCGAAAACGATTTCATGCATTTGTACTG
TTTCTGGGAGAGCTTTATCTTAACCTGGAGATCAAGGGAACAGATGGACAAGTTACGAGAGCAGGTATTCTTCAGGTTGG
TCTTCGAGAGCTGCTGAATGCCCTCTTTTCTAATCCTATGGATGACAATTTAATTTGTGCAATAAAATTATTGAAGTTGA
CAGTATCAGTTTTGGAAGATACTTGGAAGGAAAAAGGAAAGATGGATATGGAAGAAATTATTCAGAGAATTGAAAACGTT
GTCTTAGATGCAAACTGCAATAGAGATGTAAAACAGATGCTCTTGAAACTTGTGGAACTCTGGTCAAGTAACTGGGGTAG
AGTCCATGCAACTTTAACATACAGAGAAGCAACCCAGAAAGTGATCCTAACTACTTTATGAATGAACCAACATTTTATAC
ATCTGATGGTGTTCCTTTCACTGTAGCTGATCCAGATTATCAAGAGAAATATCAAGAGTTACTTGAAAGAGAGGACTTTT
TTTCCAGATTGCAAAGAAAATGGAACAGATTTATCAGGGGCTGGTGATCCATACTTGGATGATATTGATGATGAGATGGA
CCCAGAGATAGAAGAAGCTTATGAAAAGTTTTGTATGGAATCAGAGCGTAAGCAAAAACAG

Alignment

ORF - retro_cjac_3224 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 90.79 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 1
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  MAKPQVVVAPVLMSKLSVNAPEFYPSGYSSNYTESYEDGCEDYPTLSEYVQDFLNHLTEQPGSFETEIEQ
          .AKPQVVVA..LMS.L.VNAPEFY.SGYSSNYTESY.DGC.DYPTLSEYVQDFL.HLTE.PGSFETEIEQ
Retrocopy IAKPQVVVASILMSTLPVNAPEFYLSGYSSNYTESYGDGC*DYPTLSEYVQDFLDHLTEHPGSFETEIEQ

Parental  FAETLNGWVTTDDALQELVELIYQQATSIPNFSYMGARLCNYLSHHLTISPQSGNFRQLLLQRCRTEYEV
          FAETLNGW.TTD.ALQELVELIYQQ..SIPNFSY.GA.LCNYLSHHLTISPQSGNF.QLLLQRC.TEYEV
Retrocopy FAETLNGWITTDYALQELVELIYQQDMSIPNFSYIGACLCNYLSHHLTISPQSGNFCQLLLQRCWTEYEV

Parental  KDQAAKGDEVTRKRFHAFVLFLGELYLNLEIKGTNGQVTRADILQVGLRELLNALFSNPMDDNLICAVKL
          KDQAAKGDEVTRKRFHAFVLFLGELYLNLEIKGT.GQVTRA.ILQVGLRELLNALFSNPMDDNLICA.KL
Retrocopy KDQAAKGDEVTRKRFHAFVLFLGELYLNLEIKGTDGQVTRAGILQVGLRELLNALFSNPMDDNLICAIKL

Parental  LKLTGSVLEDAWKEKGKMDMEEIIQRIENVVLDANCSRDVKQMLLKLVELRSSNWGRVHATSTYREAT-P
          LKLT.SVLED.WKEKGKMDMEEIIQRIENVVLDANC.RDVKQMLLKLVEL.SSNWGRVHAT.TYREAT.P
Retrocopy LKLTVSVLEDTWKEKGKMDMEEIIQRIENVVLDANCNRDVKQMLLKLVELWSSNWGRVHATLTYREAT<P

Parental  ENDPNYFMNEPTFYTSDGVPFTAADPDYQEKYQELLERED-FFPDYEENGTDLSGAGDPYLDDIDDEMDP
          E.DPNYFMNEPTFYTSDGVPFT.ADPDYQEKYQELLERED.FFPD..ENGTDLSGAGDPYLDDIDDEMDP
Retrocopy ESDPNYFMNEPTFYTSDGVPFTVADPDYQEKYQELLERED>FFPDCKENGTDLSGAGDPYLDDIDDEMDP

Parental  EIEEAYEKFCLESERKRKQ
          EIEEAYEKFC.ESERK.KQ
Retrocopy EIEEAYEKFCMESERKQKQ

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	30.11 RPM
SRP051959_heart	0.05 RPM	38.71 RPM
SRP051959_kidney	0.04 RPM	44.99 RPM
SRP051959_liver	0.04 RPM	26.01 RPM
SRP051959_lung	0.02 RPM	30.70 RPM
SRP051959_lymph_node	0.02 RPM	29.34 RPM
SRP051959_skeletal_muscle	0.04 RPM	34.70 RPM
SRP051959_spleen	0.02 RPM	35.50 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_3224 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_3224 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_3224 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 6 parental genes, and 8 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000020376	1 retrocopy	retro_btau_359,
Choloepus hoffmanni	ENSCHOG00000004961	1 retrocopy	retro_chof_762,
Callithrix jacchus	ENSCJAG00000001340	2 retrocopies	retro_cjac_3224 , retro_cjac_3337,
Erinaceus europaeus	ENSEEUG00000009651	1 retrocopy	retro_eeur_304,
Homo sapiens	ENSG00000172239	1 retrocopy	retro_hsap_1726,
Otolemur garnettii	ENSOGAG00000001887	2 retrocopies	retro_ogar_1096, retro_ogar_1241,