RetrogeneDB ID: retro_ptro_560

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: 11:83854735..83855655(+)
• 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_560
ATGTCCGCGCCTCGAGCCCCACACGCTCTGGCGGCCGCCGCGCCAGCGTCTGGGAAGGCCAAGCTGACGCACCTGGGGAA
GGCGATCCTGGCAGGCGGCCTGGCGGGCGGCATCGAGATCTACATCACCTTCCCCACCCAGTACGTGAAGACGCAGTGGC
AGCTGGACTAGCCCTCGAACCCGCCGCGGTACCAGAGCATCGGGGACTGGGTGTGGCAGACAGTCCGCAGCCATGGCGTT
CTGGGCCTGTACCGCAGTCTCAGCTCCCTGCTCTACGGCTCCATCCCCAAAGCGGCCGCCAGCTTCGGAATGTTCTAGTT
CCTCAGCAACCACCTGCGGGATTCCCAGGGACGGCTGGACAGCACGCGCGGGCTGCTGTGCTGCCTGGGCGCTGGAGTGG
CTGAGGCCGTGGTGATCGTGTGCCCCATGGAGACCATCAAGGTGAGGTTCATCCACGACCAGACCTCCCCAAACCCCAAG
TACCCAGGATTCTTCTACGGGTTAGGAAGATTGTGCGGGAACAAGGGCTGAAGGGGATGTATCAGAGCCTCACGGCCACC
GTACTGAAACAGGGCTGGAACCAGGCCATCCGCTTCTTCGTCATGACATTCCCTGCACAACTGGTACCGAGGAGACAACC
CCAACAAGCCCATGAACCCGCTGATCACTGGGGGCTTCGGAGCCATCGTGTGCACAGCCAGCGTCTTTGGAAACACTCCT
CTGGACGTGATTAAGACCCGCAGGTAGGGCCTGGAGGCGCACAAATACCGGAACTTGATGGACTGCGGCTGGCAGATCCT
GAGGAAGGAGGAGCTCAAGGCATTCTACAAGGGCATTGTCCCGCGCTGGGCCAGGTCAGCCTGGATGTGGCCATAGTGTT
TATCATCTATGATGAGGTGGTGAAGCTGCTCAACAAAGTG

Alignment

ORF - retro_ptro_560 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 85.16 %
• Parental protein coverage: 98.71 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  MPAPRAPRALAAAAPASGKAKLTHPGKAILAGGLAGGIEICITFPTEYVKTQLQLDERSHPPRYRGIGDC
          M.APRAP.ALAAAAPASGKAKLTH.GKAILAGGLAGGIEI.ITFPT.YVKTQ.QLD..S.PPRY..IGD.
Retrocopy MSAPRAPHALAAAAPASGKAKLTHLGKAILAGGLAGGIEIYITFPTQYVKTQWQLD*PSNPPRYQSIGDW

Parental  VRQTVRSHGVLGLYRGLSSLLYGSIPKAAVRFGMFEFLSNHMRDAQGRLDSTRGLLCGLGAGVAEAVVVV
          V.QTVRSHGVLGLYR.LSSLLYGSIPKAA..FGMF.FLSNH.RD.QGRLDSTRGLLC.LGAGVAEAVV.V
Retrocopy VWQTVRSHGVLGLYRSLSSLLYGSIPKAAASFGMF*FLSNHLRDSQGRLDSTRGLLCCLGAGVAEAVVIV

Parental  CPMETIKVKFIHDQTSPNPKYRGFFHG-VREIVREQGLKGTYQGLTATVLKQGSNQAIRFFVMT-SLRNW
          CPMETIKV.FIHDQTSPNPKY.GFF.G.VR.IVREQGLKG.YQ.LTATVLKQG.NQAIRFFVMT.SL.NW
Retrocopy CPMETIKVRFIHDQTSPNPKYPGFFYG<VRKIVREQGLKGMYQSLTATVLKQGWNQAIRFFVMT>SLHNW

Parental  YRGDNPNKPMNPLITGVFGAIAGAASVFGNTPLDVIKTRMQGLEAHKYRNTWDCGLQILRKEGLKAFYKG
          YRGDNPNKPMNPLITG.FGAI...ASVFGNTPLDVIKTR..GLEAHKYRN..DCG.QILRKE.LKAFYKG
Retrocopy YRGDNPNKPMNPLITGGFGAIVCTASVFGNTPLDVIKTRR*GLEAHKYRNLMDCGWQILRKEELKAFYKG

Parental  TVPR-LGRVCLDVAIVFVIYDEVVKLLNKV
          .VPR.LG.V.LDVAIVF.IYDEVVKLLNKV
Retrocopy IVPR<LGQVSLDVAIVFIIYDEVVKLLNKV

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	0.02 RPM	25.17 RPM
SRP007412_cerebellum	0.04 RPM	15.24 RPM
SRP007412_heart	0.00 RPM	6.88 RPM
SRP007412_kidney	0.16 RPM	221.01 RPM
SRP007412_liver	0.10 RPM	129.95 RPM
SRP007412_testis	0.42 RPM	15.70 RPM

ChIP-Seq

Pan troglodytes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ptro_560 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_560 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_560 has 4 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_804
Gorilla gorilla	retro_ggor_661
Pongo abelii	retro_pabe_719
Macaca mulatta	retro_mmul_1077

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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,