RetrogeneDB ID: retro_cjac_3337

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 9:112294335..112295431(-)
• Located in intron of: ENSCJAG00000001536

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_3337
ATGGCTAAACCCCAGGTGGTTGTAGCACCTATATTAATGTCTAAGCTGTCTGTGAATGCCCCTGAATTTTATCCATCAGG
TTATTCTTCCAATTACACAGAATCCTAAGAGGATGGTTGTGAGGATTATCCCACTCTATCTGAATATGTTCAGGATTTTT
TGAATCATCTTACAGAGCAGCCTGGCAGTTTTGAAACTGAAATTGAACGGTTTGCGGAGACCCTGAATGGCTGGGTTACA
ACAGATGATGCTTTGCAAGAACTTGTGGAACTCATATCGACAGGCCACATCTATCCCGAATTTCTCTTATATGGGAGCTC
GCCTGTGTAATCACCTGTCACATCATCTGACAATTAGCCCACAGAGTGGCAACTTCCGCCAATTGCTACTTCCAAGATGT
CAGAGTGAATATGAAGTTAAAGATCAAGCTGCAAAAGGGGATGAAGTTACTCGAAAACGATTTCATGCATTTGTACTCTT
TCTGGGAGAGCTTTATCTTAACCTGGAGATCAAGGGAACAAATGGACAGGTTACGAGAGCAGATATTCTTCAGGTTGGTC
TTCGAGAGCTGCTGAATGCCCTCTTTTCTAATCCTATGGATGACAATTTAATTTGTGCAGTAAAACTATTGAAGTTGACA
GGATCAGTTTTGGAAGATCCTTGGAAGGAAAAAGGAAAGATGGATATGGAAGAAATTATTCACAGAATTGAAAATATTAT
CCTAGATGCAAACTGCAGTAGAGATGTAAAACAGATGCTCTTGAAGCTTGTGGAACTCCGGTCAAGTAACTGGGGTAGAG
TCCATGCAACTTCAACATACAGAGAAGCAACACCAAAAAATGATCCTAACTACTTTATGAATGAGCCAACATTTTATACG
TCTGATGGTGTTCCTTTCACTGCAGCTGATCCAGATTATCAAGAGAAATATCATGAGTTACTTGAAAGAGAGGACTTTTT
TCCAGATTATGAAGAAAATGGAACAGATTTATCAGGGGCTGGTGATCCATACTTGGATGATACTGATGATGAGAAGGACC
CAGAGATAGAAGAAGCTTATGAAAAGTTTTGTTTGGAATCAGAGCGTAAAGTTAAA

Alignment

ORF - retro_cjac_3337 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 92.37 %
• Parental protein coverage: 99.73 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MAKPQVVVAPVLMSKLSVNAPEFYPSGYSSNYTESYEDGCEDYPTLSEYVQDFLNHLTEQPGSFETEIEQ
          MAKPQVVVAP.LMSKLSVNAPEFYPSGYSSNYTES.EDGCEDYPTLSEYVQDFLNHLTEQPGSFETEIE.
Retrocopy MAKPQVVVAPILMSKLSVNAPEFYPSGYSSNYTES*EDGCEDYPTLSEYVQDFLNHLTEQPGSFETEIER

Parental  FAETLNGWVTTDDALQELVELIYQQATSIPNFSYMG-ARLCNYLSHHLTISPQSGNFRQLLLQRCRTEYE
          FAETLNGWVTTDDALQELVELI.......P.F...G.ARLCN.LSHHLTISPQSGNFRQLLL.RC..EYE
Retrocopy FAETLNGWVTTDDALQELVELI-STGHIYPEFLLYG>ARLCNHLSHHLTISPQSGNFRQLLLPRCQSEYE

Parental  VKDQAAKGDEVTRKRFHAFVLFLGELYLNLEIKGTNGQVTRADILQVGLRELLNALFSNPMDDNLICAVK
          VKDQAAKGDEVTRKRFHAFVLFLGELYLNLEIKGTNGQVTRADILQVGLRELLNALFSNPMDDNLICAVK
Retrocopy VKDQAAKGDEVTRKRFHAFVLFLGELYLNLEIKGTNGQVTRADILQVGLRELLNALFSNPMDDNLICAVK

Parental  LLKLTGSVLEDAWKEKGKMDMEEIIQRIENVVLDANCSRDVKQMLLKLVELRSSNWGRVHATSTYREATP
          LLKLTGSVLED.WKEKGKMDMEEII.RIEN..LDANCSRDVKQMLLKLVELRSSNWGRVHATSTYREATP
Retrocopy LLKLTGSVLEDPWKEKGKMDMEEIIHRIENIILDANCSRDVKQMLLKLVELRSSNWGRVHATSTYREATP

Parental  ENDPNYFMNEPTFYTSDGVPFTAADPDYQEKYQELLEREDFFPDYEENGTDLSGAGDPYLDDIDDEMDPE
          .NDPNYFMNEPTFYTSDGVPFTAADPDYQEKY.ELLEREDFFPDYEENGTDLSGAGDPYLDD.DDE.DPE
Retrocopy KNDPNYFMNEPTFYTSDGVPFTAADPDYQEKYHELLEREDFFPDYEENGTDLSGAGDPYLDDTDDEKDPE

Parental  IEEAYEKFCLESERKRK
          IEEAYEKFCLESERK.K
Retrocopy IEEAYEKFCLESERKVK

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	0.38 RPM	30.11 RPM
SRP051959_heart	0.40 RPM	38.71 RPM
SRP051959_kidney	0.60 RPM	44.99 RPM
SRP051959_liver	0.61 RPM	26.01 RPM
SRP051959_lung	0.52 RPM	30.70 RPM
SRP051959_lymph_node	1.19 RPM	29.34 RPM
SRP051959_skeletal_muscle	0.28 RPM	34.70 RPM
SRP051959_spleen	0.71 RPM	35.50 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_3337 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_3337 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_3337 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,