RetrogeneDB ID: retro_ptro_1139

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: 16:45169770..45170262(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: SLC25A1
• Ensembl ID: ENSPTRG00000014057
• Aliases: None
• Description: None

Sequence

>retro_ptro_1139
GGCCTCAGCTCCCTGTTCTGCGGCTCCATCCCCGAGGCAGAGTCAGGTTCGGGAAGTTGGAGTTCCTCTGCACCCAGATG
TGGAATGCCCAGGGAATGCTGAACAGCAGGCGCGGGCTGCTGTGAGGCCTAGACACCGGCGTGGCCGAGGCCATGGTGGT
CGTACGTCCCATGGAGACCATCAAAGTGAAGTTCATCCACTACCGGACCTCCCCAAACCCAAGAACAGATAATTCTTCGG
GGTTAGGGAGATTGTGCGGGAACAAGGGCTGAGGGGACTTACCAGGGCCTCAGGGCCGCCGGGCTGAAGCAGGGCTGGAA
CCAGGCCATTGTTTCTTTGTCCTGACCTCCCTGCAGCAACTGGTACCGAAGAGATAAGCCCATGAACCCGCTGATCACTG
GGGTCTTCTGAGCCATTGCAGGCACAGCCAGCGTCTTCGGAAACACCCCTCTGGACGGGATCCCGAGGGGCTCAAGGCCT
TCACAAGGGCAC

Alignment

ORF - retro_ptro_1139 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 69.54 %
• Parental protein coverage: 54.34 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 5

Retrocopy - Parental Gene Alignment:

Parental  GLSSLLYGSIPKAA-VRFGMFEFLSNHMRDAQGRLDSTRGLLCGLGAGVAEAVVVVCPMETIKVKFIHDQ
          GLSSL..GSIP.A..VRFG..EFL...M..AQG.L.S.RGLL.GL..GVAEA.VVV.PMETIKVKFIH..
Retrocopy GLSSLFCGSIPEAE<VRFGKLEFLCTQMWNAQGMLNSRRGLL*GLDTGVAEAMVVVRPMETIKVKFIHYR

Parental  TSPN-PKYRGFFHGVREIVREQGLK-GTYQGLTATVLKQGSNQAI-RFFVMTSLR-NWYRGDNPNKPMNP
          TSPN.PK.R.FF.GVREIVREQGL..GTYQGL.A..LKQG.NQAI..FFV.TSL..NWYR.D...KPMNP
Retrocopy TSPN<PKNR*FF-GVREIVREQGLR<GTYQGLRAAGLKQGWNQAI<CFFVLTSLQ>NWYRRD---KPMNP

Parental  LITGVFGAIAGAASVFGNTPLDVIKTRMQGLEAH
          LITGVF.AIAG.ASVFGNTPLD.I.........H
Retrocopy LITGVF*AIAGTASVFGNTPLDGIPRGSRPSQGH

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	0.00 RPM	25.17 RPM
SRP007412_cerebellum	0.00 RPM	15.24 RPM
SRP007412_heart	0.00 RPM	6.88 RPM
SRP007412_kidney	0.00 RPM	221.01 RPM
SRP007412_liver	0.00 RPM	129.95 RPM
SRP007412_testis	0.00 RPM	15.70 RPM

ChIP-Seq

Pan troglodytes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ptro_1139 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_1139 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_1139 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 8 parental genes, and 24 retrocopies.

Species	Parental gene accession	Retrocopies number
Homo sapiens	ENSG00000100075	2 retrocopies	retro_hsap_1632, retro_hsap_804,
Gorilla gorilla	ENSGGOG00000006198	2 retrocopies	retro_ggor_1230, retro_ggor_661,
Macaca mulatta	ENSMMUG00000005431	4 retrocopies	retro_mmul_1077, retro_mmul_1556, retro_mmul_1683, retro_mmul_485,
Nomascus leucogenys	ENSNLEG00000005215	2 retrocopies	retro_nleu_2866, retro_nleu_408,
Ochotona princeps	ENSOPRG00000011649	1 retrocopy	retro_opri_1053,
Pongo abelii	ENSPPYG00000029785	9 retrocopies	retro_pabe_1346, retro_pabe_1414, retro_pabe_1529, retro_pabe_1671, retro_pabe_3125, retro_pabe_3217, retro_pabe_334, retro_pabe_3564, retro_pabe_719,
Pan troglodytes	ENSPTRG00000014057	3 retrocopies	retro_ptro_1139 , retro_ptro_1364, retro_ptro_560,
Tursiops truncatus	ENSTTRG00000006845	1 retrocopy	retro_ttru_228,