RetrogeneDB ID: retro_cjac_2820

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 6:81307834..81308532(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSCJAG00000031429
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: IDI1
• Ensembl ID: ENSCJAG00000008483
• Aliases: None
• Description: isopentenyl-diphosphate delta isomerase 1 [Source:HGNC Symbol;Acc:5387]

Sequence

>retro_cjac_2820
CAGATCAGACATTTTGTAATGATGCCTGAAATAAACACTGACCACCCCGACGAAGAACAGGTTCAACTCCTGGGAGGGAT
GTGTAACCTTATTAATGAAAATGACAATAAAATTGGGGCTGAGACCAAGAAGAACTGTCATTTGAATGAGAATATCGAGA
AAGGATTATTGCATCGAGCTTTTAGTGTCTTCTTATTCAACACTGAAAATAAGCTTCTGCTACAAGATCAGATGCTAAGA
TTACCTTTCCAGGTTGTTTTACTAATACTTGTTGTAATCATACATTAAGTAATCAGGTGAGCTAGAGGAAAATGGTGCCC
TTGGAGTGAGACAAGCAGCACAGAGGTGGCTGAAAGCTGAGCTAGGAATTCCCTTGGCAGAGGTTACTCCAGAAGAAACT
AATTATTTAACACGAATTCACTACAAAGCTCAGCAGGATAGTATCTGGGGTGAACAGGAAATTGATTATATTTTATTTGT
GAAGAAGAATATAACTTTGAATCCAGATCCCAATGAGATTAAAATATATTGTTAGGTGTCAAAGGAAGAACCAAAAGAAC
TTTGGGAAAAAAGCAGCTAATGGTGAAATTAAGATAATGCCATGGTTTCAAATTATTGCAGAGACTTTTCTCTTTAAATG
GTGGGATAACTTAAATCATTTGAATCAGTTTGTTGACCATGAGAAAATATACAGAATG

Alignment

ORF - retro_cjac_2820 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 85.23 %
• Parental protein coverage: 82.39 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  QIRHFVMMPEINTDHLDEQQVQLLAEMCILIDENDNKIGAETKKNCHLNENIDKGLLHRAFSVFLFNTEN
          QIRHFVMMPEINTDH.DE.QVQLL..MC.LI.ENDNKIGAETKKNCHLNENI.KGLLHRAFSVFLFNTEN
Retrocopy QIRHFVMMPEINTDHPDEEQVQLLGGMCNLINENDNKIGAETKKNCHLNENIEKGLLHRAFSVFLFNTEN

Parental  KLLLQQ-RSDAKITFPGCFTNTCCSHPLSNP-GELEENDALGVKRAAQRRLKAELGIPLEQVPPEEINYL
          K.LL.Q.RSDAKITFPGCFTNTCC.H.LSN..GELEEN.ALGV..AAQR.LKAELGIPL..V.PEE.NYL
Retrocopy K-LLLQ<RSDAKITFPGCFTNTCCNHTLSNQ<GELEENGALGVRQAAQRWLKAELGIPLAEVTPEETNYL

Parental  TRIYYKAQSDGIWGEHEIDYILFVKKNVTLNPDPNEIKSYCYVSKEELKELL-KKAASGEIKITPWFQII
          TRI.YKAQ.D.IWGE.EIDYILFVKKN.TLNPDPNEIK.YC.VSKEE.KEL..KKAA.GEIKI.PWFQII
Retrocopy TRIHYKAQQDSIWGEQEIDYILFVKKNITLNPDPNEIKIYC*VSKEEPKELW>KKAANGEIKIMPWFQII

Parental  AETFLFKWWDNLNHLNQFVDHEKIHRM
          AETFLFKWWDNLNHLNQFVDHEKI.RM
Retrocopy AETFLFKWWDNLNHLNQFVDHEKIYRM

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	0.49 RPM	10.67 RPM
SRP051959_heart	0.30 RPM	2.16 RPM
SRP051959_kidney	0.38 RPM	4.50 RPM
SRP051959_liver	0.48 RPM	53.98 RPM
SRP051959_lung	0.31 RPM	2.60 RPM
SRP051959_lymph_node	0.25 RPM	3.06 RPM
SRP051959_skeletal_muscle	0.11 RPM	2.56 RPM
SRP051959_spleen	0.48 RPM	2.77 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_2820 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_2820 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_2820 has 4 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_2161
Pan troglodytes	retro_ptro_1647
Gorilla gorilla	retro_ggor_1717
Macaca mulatta	retro_mmul_899

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Parental genes homology:

Parental genes homology involve 14 parental genes, and 37 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000008483	3 retrocopies	retro_cjac_2083, retro_cjac_2591, retro_cjac_2820 ,
Erinaceus europaeus	ENSEEUG00000012555	3 retrocopies	retro_eeur_188, retro_eeur_198, retro_eeur_61,
Homo sapiens	ENSG00000067064	3 retrocopies	retro_hsap_2161, retro_hsap_2444, retro_hsap_4053,
Gorilla gorilla	ENSGGOG00000000934	3 retrocopies	retro_ggor_1521, retro_ggor_1717, retro_ggor_2722,
Macaca mulatta	ENSMMUG00000017115	3 retrocopies	retro_mmul_2340, retro_mmul_632, retro_mmul_899,
Monodelphis domestica	ENSMODG00000005998	5 retrocopies	retro_mdom_1107, retro_mdom_1692, retro_mdom_1697, retro_mdom_1724, retro_mdom_547,
Mus musculus	ENSMUSG00000058258	4 retrocopies	retro_mmus_2032, retro_mmus_2660, retro_mmus_417, retro_mmus_552,
Nomascus leucogenys	ENSNLEG00000013594	3 retrocopies	retro_nleu_1810, retro_nleu_2777, retro_nleu_2804,
Oryctolagus cuniculus	ENSOCUG00000007493	1 retrocopy	retro_ocun_267,
Ochotona princeps	ENSOPRG00000008692	2 retrocopies	retro_opri_694, retro_opri_755,
Pongo abelii	ENSPPYG00000002039	2 retrocopies	retro_pabe_1783, retro_pabe_3327,
Pan troglodytes	ENSPTRG00000002239	3 retrocopies	retro_ptro_1412, retro_ptro_1647, retro_ptro_2747,
Ictidomys tridecemlineatus	ENSSTOG00000023260	1 retrocopy	retro_itri_118,
Tursiops truncatus	ENSTTRG00000011174	1 retrocopy	retro_ttru_255,