RetrogeneDB ID: retro_mmul_1365

Retrocopy location

• Organism: Rhesus macaque (Macaca mulatta)
• Coordinates: 19:19519509..19519891(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSMMUG00000017589
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: ISCA1
• Ensembl ID: ENSMMUG00000003399
• Aliases: None
• Description: None

Sequence

>retro_mmul_1365
TCGGCTTCCTTAGTCCCGGCAACTGTCTGGGCTGTAAGCAAGAGGAAGCGTCAGCCCACCCGGACCGCCCTCGCCCTGAC
ACCTTCAGCAGTAAACAAGATAAAACAACTTCTTAAAGATAAGCCTGAGCATGTAGGTGTAAAAGTTGGTGTGCGAGCCA
GGGGCTGTAATGGCCTTTCTTATGCTCTAGAATACAGGAAGACAAAAGGAGATTCCAACGAAGAAGTTATTCAAGATGGA
GTCAGAGTATTCATTGAAAAGAAAGCACAGCTAAACTTTTAGACCAGAAATGGACTATGTTGAAGAAAAATTATCCAGTG
AGTCTGTGTTCAATAACCCAAACATCAAAAGAACTTGTGGCTGTGGAGAAAGCTTTAATATT

Alignment

ORF - retro_mmul_1365 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 83.85 %
• Parental protein coverage: 99.22 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  SASLVRATVRAVSKRKLQPTRAALTLTPSAVNKIKQLLKDKPEHVGVKVGVRTRGCNGLSYTLEYTKTKG
          SASLV.ATV.AVSKRK.QPTR.AL.LTPSAVNKIKQLLKDKPEHVGVKVGVR.RGCNGLSY.LEY.KTKG
Retrocopy SASLVPATVWAVSKRKRQPTRTALALTPSAVNKIKQLLKDKPEHVGVKVGVRARGCNGLSYALEYRKTKG

Parental  DSDEEVIQDGVRVFIE-KKAQLTLLGT-EMDYVEDKLSSEFVFNNPNIKGTCGCGESFNI
          DS.EEVIQDGVRVFIE.K.....LL...EMDYVE.KLSSE.VFNNPNIK.TCGCGESFNI
Retrocopy DSNEEVIQDGVRVFIE<KESTAKLLDQ<EMDYVEEKLSSESVFNNPNIKRTCGCGESFNI

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
SRP007412_brain	0.00 RPM	97.93 RPM
SRP007412_brain_prefrontal_cortex	0.16 RPM	82.50 RPM
SRP007412_cerebellum	0.13 RPM	76.20 RPM
SRP007412_heart	0.00 RPM	49.52 RPM
SRP007412_kidney	0.12 RPM	49.29 RPM
SRP007412_liver	0.00 RPM	16.51 RPM
SRP007412_testis	0.04 RPM	53.15 RPM

ChIP-Seq

Macaca mulatta was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_mmul_1365 retrocopy.

TSS

Macaca mulatta was not studied using FANTOM5 data.

Lab

retro_mmul_1365 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmul_1365 has 1 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_1975

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Parental genes homology:

Parental genes homology involve 13 parental genes, and 45 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000046526	2 retrocopies	retro_btau_1787, retro_btau_506,
Callithrix jacchus	ENSCJAG00000001940	6 retrocopies	retro_cjac_1623, retro_cjac_1734, retro_cjac_1870, retro_cjac_2608, retro_cjac_350, retro_cjac_672,
Dasypus novemcinctus	ENSDNOG00000010652	5 retrocopies	retro_dnov_1162, retro_dnov_142, retro_dnov_1956, retro_dnov_431, retro_dnov_95,
Echinops telfairi	ENSETEG00000016537	1 retrocopy	retro_etel_1857,
Homo sapiens	ENSG00000135070	6 retrocopies	retro_hsap_1556, retro_hsap_1768, retro_hsap_1975, retro_hsap_2314, retro_hsap_317, retro_hsap_3329,
Gorilla gorilla	ENSGGOG00000007518	2 retrocopies	retro_ggor_1182, retro_ggor_92,
Macaca mulatta	ENSMMUG00000003399	3 retrocopies	retro_mmul_1230, retro_mmul_1365 , retro_mmul_2211,
Monodelphis domestica	ENSMODG00000003559	1 retrocopy	retro_mdom_583,
Mus musculus	ENSMUSG00000044792	1 retrocopy	retro_mmus_278,
Pongo abelii	ENSPPYG00000019339	5 retrocopies	retro_pabe_1287, retro_pabe_2043, retro_pabe_2744, retro_pabe_2745, retro_pabe_367,
Pan troglodytes	ENSPTRG00000021075	7 retrocopies	retro_ptro_1047, retro_ptro_1185, retro_ptro_1316, retro_ptro_1689, retro_ptro_2149, retro_ptro_256, retro_ptro_2842,
Rattus norvegicus	ENSRNOG00000018343	4 retrocopies	retro_rnor_1177, retro_rnor_1805, retro_rnor_2254, retro_rnor_2956,
Tarsius syrichta	ENSTSYG00000012826	2 retrocopies	retro_tsyr_1060, retro_tsyr_1698,