RetrogeneDB ID: retro_ptro_1047

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: 15:37852641..37853047(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: ISCA1
• Ensembl ID: ENSPTRG00000021075
• Aliases: None
• Description: Pan troglodytes iron-sulfur cluster assembly 1 homolog (S. cerevisiae) (ISCA1), mRNA. [Source:RefSeq mRNA;Acc:NM_001242612]

Sequence

>retro_ptro_1047
AGGCCTGAGTGCGCTGTGTGCCGGAGCTTGTGGCATCAATGGGCCTGCTGTGTCCAAAGAAAGAGGCTGAGGCAGCCGAG
CTCCGGCCTGAAGCACCTGGACCAGACGACAAAGAGGTCGGCTTCCTTAGTCCGGAGGACTGTCCGGACTGTGAGCAAGA
GGAAGCTACAGCCCACGAGGGCCACCCGCAGCCTGACACCTTCAGCAGTAAACAAGATAAAATAACTTCTTCAAGATAAG
CCTGAGTATTAGGTGTAAAAGTTGGTGTCCGAACCAGGGCCTGTAATGACCTTTCTTATAGTCTAGAATAAACGAAGACA
AGGGAGATTTCGATGAAGAAGTCATTCAAGATGGAGTCAGAGTGTTCATCGAAAAGAAAGCACAACTAACACTTTTAGGA
ACAGAA

Alignment

ORF - retro_ptro_1047 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 71.94 %
• Parental protein coverage: 77.84 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  RTEGAVRRSLWRQCARRVHGEKLRRQTFGPRHRGAGTAKMSASLVRATVRAVSKRKLQPTRAALTLTPSA
          R.E.AV.RSLW.Q.A..V....LR....G..H....T.K.SASLVR.TVR.VSKRKLQPTRA...LTPSA
Retrocopy RPECAVCRSLWHQWACCVQRKRLRQPSSGLKHLDQ-TTKRSASLVRRTVRTVSKRKLQPTRATRSLTPSA

Parental  VNKIKQLLKDKPEH-VGVKVGVRTRGCNGLSYTLEYTKT-KGDSDEEVIQDGVRVFIEKKAQLTLLGTE
          VNKIK.LL.DKPE...GVKVGVRTR.CN.LSY.LE.TKT.KGD.DEEVIQDGVRVFIEKKAQLTLLGTE
Retrocopy VNKIK*LLQDKPEY<LGVKVGVRTRACNDLSYSLE*TKT<KGDFDEEVIQDGVRVFIEKKAQLTLLGTE

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_prefrontal_cortex	0.07 RPM	38.84 RPM
SRP007412_cerebellum	0.00 RPM	15.67 RPM
SRP007412_heart	0.03 RPM	11.86 RPM
SRP007412_kidney	0.10 RPM	15.38 RPM
SRP007412_liver	0.10 RPM	5.04 RPM
SRP007412_testis	0.11 RPM	8.54 RPM

ChIP-Seq

Pan troglodytes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ptro_1047 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_1047 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_1047 has 4 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_1556
Gorilla gorilla	retro_ggor_1182
Pongo abelii	retro_pabe_1287
Macaca mulatta	retro_mmul_2211

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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,