RetrogeneDB ID: retro_cjac_1453

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 16:22105249..22105814(+)
• Located in intron of: ENSCJAG00000005106

Retrocopy information

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

Parental gene information

• Parental gene symbol: TMX1
• Ensembl ID: ENSCJAG00000006893
• Aliases: None
• Description: thioredoxin-related transmembrane protein 1 [Source:HGNC Symbol;Acc:15487]

Sequence

>retro_cjac_1453
CACAGGTGGCAGAGAGATGTACACATTATCATAGATGAGAACCTAAGACAGTTGTTGGAAGGAGATTGGATGATAGAATT
TTAGGCCTCATGGTACCCTGCTTGTCAAAATCTTCAACCAGAATGGAAACTTTTGCTGAATGGGGAAAAGATCTTGACGT
TAATGTTGCAAAAGTAGATGTCACAGGGCAGCCAGGACTGAGTAGAGAGTTCATCATAACTGCTCTCCTACTATTTATCA
TTGTAAAGATGGTGAATTTAGGCACCATCAAGGTCCAAGGACTATGAAACACTTCAGAAACTTTGTAAGTGATAAAGAGT
AGAAGAGTATTGAATCAGTTCCATCATGGCTTGGTTTGGGTTCCTTTCTGATGAACAATATGTCAGCACTCTTTCAGCTC
TCTATGTGGATCAGGATTTGCCATAACTAACTTATTGAAAACTTTGAATTACCGGTTTTGAAATTGTATACAGCTTTTGC
TTTAGCAATTCTTCTTTCAGAACTGTTTTTAGGACTCTGTATGATATTTGTGGCAGATTGCTTTTGTCCTTCAAAAAGGC
GCAGA

Alignment

ORF - retro_cjac_1453 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 73.3 %
• Parental protein coverage: 68.23 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  HGRRSNVRVITDENWRELLEGDWMIEFYAPWCPACQNLQPEW-ESFAEWGEDLEVNVAKVDVTEQPGLSG
          H.....V..I.DEN.R.LLEGDWMIEF.A.W.PACQNLQPEW.E.FAEWG.DL.VNVAKVDVT.QPGLS.
Retrocopy HRWQRDVHIIIDENLRQLLEGDWMIEF*ASWYPACQNLQPEW<ETFAEWGKDLDVNVAKVDVTGQPGLSR

Parental  RFIITAL-PTIYHCKDGEFRRYQGPRTKKDFINFISDKEWKSIEPVSSWFGPDSVLMSSMSALFQLSMWI
          .FIITAL.PTIYHCKDGEFR..QGPRT.K.F.NF.SDKE.KSIE.V.SW.G..S.LM..MSALFQLSMWI
Retrocopy EFIITAL<PTIYHCKDGEFRHHQGPRTMKHFRNFVSDKE*KSIESVPSWLGLGSFLMNNMSALFQLSMWI

Parental  RTCHNYFIEDLGLPVWGSYTIFALVTLLSGLLLGLCMIFVADCLCPSKRRR
          R.CHN..IE...LPV...YT.FAL..LLS.L.LGLCMIFVADC.CPSKRRR
Retrocopy RICHN*LIENFELPVLKLYTAFALAILLSELFLGLCMIFVADCFCPSKRRR

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	0.02 RPM	36.32 RPM
SRP051959_heart	0.58 RPM	21.86 RPM
SRP051959_kidney	0.02 RPM	34.85 RPM
SRP051959_liver	0.02 RPM	25.04 RPM
SRP051959_lung	0.07 RPM	37.29 RPM
SRP051959_lymph_node	0.07 RPM	57.81 RPM
SRP051959_skeletal_muscle	0.41 RPM	13.82 RPM
SRP051959_spleen	0.06 RPM	57.77 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_1453 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_1453 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_1453 has 2 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_3970
Pan troglodytes	retro_ptro_2695

---

Parental genes homology:

Parental genes homology involve 14 parental genes, and 18 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000015041	1 retrocopy	retro_amel_719,
Canis familiaris	ENSCAFG00000014626	1 retrocopy	retro_cfam_796,
Choloepus hoffmanni	ENSCHOG00000011305	1 retrocopy	retro_chof_1249,
Callithrix jacchus	ENSCJAG00000006893	1 retrocopy	retro_cjac_1453 ,
Dasypus novemcinctus	ENSDNOG00000016496	1 retrocopy	retro_dnov_78,
Felis catus	ENSFCAG00000002780	1 retrocopy	retro_fcat_333,
Homo sapiens	ENSG00000139921	2 retrocopies	retro_hsap_3840, retro_hsap_3970,
Gorilla gorilla	ENSGGOG00000009768	1 retrocopy	retro_ggor_2587,
Loxodonta africana	ENSLAFG00000013251	1 retrocopy	retro_lafr_1214,
Macaca mulatta	ENSMMUG00000001901	1 retrocopy	retro_mmul_1618,
Nomascus leucogenys	ENSNLEG00000012362	2 retrocopies	retro_nleu_1976, retro_nleu_2524,
Oryctolagus cuniculus	ENSOCUG00000003980	1 retrocopy	retro_ocun_571,
Pongo abelii	ENSPPYG00000005810	2 retrocopies	retro_pabe_3058, retro_pabe_3264,
Pan troglodytes	ENSPTRG00000006339	2 retrocopies	retro_ptro_2522, retro_ptro_2695,