RetrogeneDB ID: retro_cjac_3330

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 9:100651038..100651653(-)
• Located in intron of: ENSCJAG00000009289

Retrocopy information

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

Parental gene information

• Parental gene symbol: FOLR1
• Ensembl ID: ENSCJAG00000015224
• Aliases: None
• Description: folate receptor 1 (adult) [Source:HGNC Symbol;Acc:3791]

Sequence

>retro_cjac_3330
GAGAGCCACCTCCTCTCCCAGTGTTGTCCCTGGAGGAATGCCTGCTGTTCTACCAATACCAGCCAGGAAGCCCACAAGGA
TGTTTCCTACCTACACAACTTCAACTGGAACCACTTCGGAGAGATGGCACCTGCCTGCAAACGGCATTTCATCCAGGACA
CCTGCCTCTATGAGTGCTCCCCCAGCTTGGGGCCCTGGATTCAGCAGGTGGATCAGAGCTGGCGTAAAGAGCGGGTACTG
GACGTGCCCCTGTGCAAAGAGGACTGTGAACAATGGTGGAAACATTGTGGTACCTCCTATACCTGCAAGAGCAACTGGCA
CAAGGGCTGGAATTGGACCTCAGGGTCTAACAAGTGCCCGGTGGGAGCTGCCTGCCTACCTTTCCATTTCTACTTCCCCA
CACCCACTGCTCTGTGCAATGAAATCTTGAGTCCCTCCTTCAAGATCAGCAACTACAGCCAAGGGAGCGGCCGCTGCATC
CAGATGTGATTCCACCCAGACCAGGGCAACACCAACGAGGAGGTGGCAAGGTTCTATGCTGCGGCCATGAGTGGGGCTGG
GCCCTGGGCGGCCTGTCCTGTCCTGCTCAGCCTGGGCCTGCTCTGGCTGCTCAGC

Alignment

ORF - retro_cjac_3330 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 90.29 %
• Parental protein coverage: 80.78 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  EDKLHEQCRPWRKNACCSTNTSQEAHKDVSYLYNFNWNHCGEMAPACKRHFIQDTCLYECSPNLGPWIQQ
          E..L..QC.PWR.NACCSTNTSQEAHKDVSYL.NFNWNH.GEMAPACKRHFIQDTCLYECSP.LGPWIQQ
Retrocopy ESHLLSQCCPWR-NACCSTNTSQEAHKDVSYLHNFNWNHFGEMAPACKRHFIQDTCLYECSPSLGPWIQQ

Parental  VDQSWRKERVLDVPLCKEDCEQWWKDCNTSKTCKSNWHKGWNWTSGSNKCPVGAACLPFHSYFPTPTALC
          VDQSWRKERVLDVPLCKEDCEQWWK.C.TS.TCKSNWHKGWNWTSGSNKCPVGAACLPFH.YFPTPTALC
Retrocopy VDQSWRKERVLDVPLCKEDCEQWWKHCGTSYTCKSNWHKGWNWTSGSNKCPVGAACLPFHFYFPTPTALC

Parental  NEIWSHSFKVSNYSRGSGRCIQMWFDPDQGNPNEEVARFYAAAMSGAGPWAACPVLLSLGLLWLLS
          NEI.S.SFK.SNYS.GSGRCIQM.F.PDQGN.NEEVARFYAAAMSGAGPWAACPVLLSLGLLWLLS
Retrocopy NEILSPSFKISNYSQGSGRCIQM*FHPDQGNTNEEVARFYAAAMSGAGPWAACPVLLSLGLLWLLS

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	0.16 RPM	0.07 RPM
SRP051959_heart	0.09 RPM	0.00 RPM
SRP051959_kidney	0.11 RPM	18.66 RPM
SRP051959_liver	0.04 RPM	0.02 RPM
SRP051959_lung	0.08 RPM	0.44 RPM
SRP051959_lymph_node	0.07 RPM	0.05 RPM
SRP051959_skeletal_muscle	0.13 RPM	0.00 RPM
SRP051959_spleen	0.23 RPM	0.11 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_3330 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_3330 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_3330 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 12 parental genes, and 20 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000005777	1 retrocopy	retro_cfam_1723,
Callithrix jacchus	ENSCJAG00000015224	1 retrocopy	retro_cjac_3330 ,
Dasypus novemcinctus	ENSDNOG00000000856	1 retrocopy	retro_dnov_1751,
Echinops telfairi	ENSETEG00000015365	2 retrocopies	retro_etel_1160, retro_etel_128,
Myotis lucifugus	ENSMLUG00000014126	2 retrocopies	retro_mluc_1199, retro_mluc_567,
Monodelphis domestica	ENSMODG00000008017	1 retrocopy	retro_mdom_990,
Monodelphis domestica	ENSMODG00000008032	1 retrocopy	retro_mdom_588,
Monodelphis domestica	ENSMODG00000008042	1 retrocopy	retro_mdom_648,
Mus musculus	ENSMUSG00000001827	1 retrocopy	retro_mmus_1438,
Oryctolagus cuniculus	ENSOCUG00000000165	1 retrocopy	retro_ocun_472,
Otolemur garnettii	ENSOGAG00000000641	5 retrocopies	retro_ogar_2539, retro_ogar_2666, retro_ogar_2758, retro_ogar_2908, retro_ogar_532,
Tarsius syrichta	ENSTSYG00000003503	3 retrocopies	retro_tsyr_1057, retro_tsyr_111, retro_tsyr_1651,