RetrogeneDB ID: retro_cjac_3285

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 9:25795060..25795655(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: MESDC2
• Ensembl ID: ENSCJAG00000007811
• Aliases: None
• Description: mesoderm development candidate 2 [Source:HGNC Symbol;Acc:13520]

Sequence

>retro_cjac_3285
AGCTGGATGTGCATCGAAATGGTCCTGATTCATGCCTCTGGCCTGTTGCTGCTGCAGCAGCTACCTGAGGCTTGTGCAGC
CAAGGGCCCAGCCAGAACACCCAGTAAGTGTTCACATCCCCAGAAGAAGAAGTACATTCATGATTACAATGATGTAGACA
TGGCATGTATTCTGGTAGAGTGGGAGAAAGATGATGACATAAGAAAAGACCTTCCAGAGCACAGGAGACCCTCACTACCT
GTCAATTTCTTATATTTAGACATGAACAAGCCTGAGAGATTATTGAAAATGATGAATAAAAGGAAAGATTCTTATAGTTT
GTCACTGTATCAGGAAGCCCCACTGAGGAGACAGAGGAAAACATGAGCTTCTGTCAGGACGGGCTTTTCAATGCTAACGA
GATGTCCAGAGGTTCACTGTGGGATCAGACCATACTATCTTCATGCTTCATGATTGAAAACATGCCTGGGAGATCGAGAA
CTTGTCAGTCAAGACGTGTGCTAATTCAACTCTGGAGGGGCAGGTGTACCCTGGCAAAGGAGAAGGAAGCAAAGACAAGA
ATAAAGCAAGACAACAGTGAAAAGAAGAAAAGAGA

Alignment

ORF - retro_cjac_3285 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 56.25 %
• Parental protein coverage: 88.79 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  TWARKAVVLLCASDLLLLLLPPPGACTAEGSSGTPDESTPPPRKKKKDIRDYNDADMARLLEQWEKDDDI
          .W.....VL..AS.LLLL...P..AC.A.G...TP.....P...KKK.I.DYND.DMA..L..WEKDDDI
Retrocopy SWMCIEMVLIHASGLLLLQQLPE-ACAAKGPARTPSKCSHP--QKKKYIHDYNDVDMACILVEWEKDDDI

Parental  EEGDLPEHKRPSAPVDFSKIDPSKPESILKMTKKGKT-LMMFVTVSGSPTEKETEEITSLWQGSLFNANY
          ...DLPEH.RPS.PV.F...D..KPE..LKM..K.K.....FVTVSGSPTE.ETEE..S..Q..LFNAN.
Retrocopy RK-DLPEHRRPSLPVNFLYLDMNKPERLLKMMNKRKD<FL*FVTVSGSPTE-ETEENMSFCQDGLFNANE

Parental  -DVQRFIVGSDRAIFMLRDGSYAWEIKDFLVSQDRCADVTLEGQVYPGKGGGSKEKNKTKQDKGKKKK
          .DVQRF.VGSD..IFML.D...AWEI....V....CA..TLEGQVYPGKG.GSK.KNK..Q.....K.
Retrocopy <DVQRFTVGSDHTIFMLHD*KHAWEIENLSVKT--CANSTLEGQVYPGKGEGSKDKNKARQQ*KEEKR

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	9.05 RPM
SRP051959_heart	0.02 RPM	9.65 RPM
SRP051959_kidney	0.04 RPM	23.14 RPM
SRP051959_liver	0.00 RPM	20.19 RPM
SRP051959_lung	0.00 RPM	12.54 RPM
SRP051959_lymph_node	0.00 RPM	14.75 RPM
SRP051959_skeletal_muscle	0.02 RPM	6.75 RPM
SRP051959_spleen	0.02 RPM	15.13 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_3285 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_3285 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_3285 has 3 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_990
Pan troglodytes	retro_ptro_759
Gorilla gorilla	retro_ggor_793

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Parental genes homology:

Parental genes homology involve 7 parental genes, and 8 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000007811	1 retrocopy	retro_cjac_3285 ,
Homo sapiens	ENSG00000117899	1 retrocopy	retro_hsap_990,
Gorilla gorilla	ENSGGOG00000027583	1 retrocopy	retro_ggor_793,
Loxodonta africana	ENSLAFG00000014513	1 retrocopy	retro_lafr_505,
Monodelphis domestica	ENSMODG00000019402	2 retrocopies	retro_mdom_30, retro_mdom_344,
Oryctolagus cuniculus	ENSOCUG00000016290	1 retrocopy	retro_ocun_1947,
Pan troglodytes	ENSPTRG00000007366	1 retrocopy	retro_ptro_759,