RetrogeneDB ID: retro_ptro_3158

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: X:116272062..116273297(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: ASS1
• Ensembl ID: ENSPTRG00000021473
• Aliases: None
• Description: None

Sequence

>retro_ptro_3158
ATGTCCAGCAAAGGCTCTGTGGTTCTGGCCTACAGTGGCGGCCTGGACACCTCCTGCATCCTCGTGTTACTGAAGGAACA
AGGCTATGACATCATTGCCTACGTGAACAACACTGGCCAGAAGGAAGACTTTGAGGAAGCCAGGAAGAAGGCACTGAAGC
TTGGGGGCAAAAAGGTGTTCATTGAGGAAGTCAGCAAGGAGTTTGTGAAGGAGTTCATCTGGCTGGCCATCCAGTCCAGC
GCGCTGTATGAGGACCGCTACCTCCTGGGCACCTCTCTCACCAGGCCCTGCATCGCCCGAAAACAAGTGGAAATCGCCCA
GCAGGAGAGGGCCAAGTAAGTGTCCCACGGCGCCACAGGAAAGGGAAATGATCAGGTCCAGTTTGAGCTAAACTGCTACT
CTCTGGCCCCCCAGATAAAGGTCATTGCTCCCTGGAGGATGCCCAAGTTCTACAACAGGTTCAAGGTCCGAAATGACCTT
ATGGAACACACAAAGCAACACGGGATTCCCATCCCAGTCACTCCCAAGAACCCGTGGAGCATGGACGAGAACCTCATGCA
GATCAGCAATGAGGCTGGAATCTTGGAGAACCCTAAGAACCAAGCATTTCCAGGTCTCTCCACGAAGACCCAGGACCCGG
CCAAAGCCCCCAGAACCCCTGACATTCTCGAGATCGAGTTCAAATAAGGAGTCCCCGTGAAAGTGACCAATGTCAAGGAT
GGCACCACCCACCAGACCTCCTTGGAGCTCTTCCTGTACATAAGCGAAGACGCGGGCAAGTACAGCTTGGGCCGTATTGA
CATCAAGGAGAACCACTTCACTGGAATGAAGTCCCCAGGTATCTATGAGACCCCAGCAGACACCATCGTTTACCATGCTC
ATTTAGACATCAGGGCCTTCACCATGGACCGGGAAGTATGCAAAATCAAATAAGGCCTGGGCTTGAAATTTGCTGAGCTG
GTGTATTCTGGTTTCTGGCACAGCCTTGAGTGTAAATTTGTCCACCACTGCATTACCAAGTCCCAGGAGTGAGTGGAAGG
GAAAGTGCAGGTGTCCGTCTTCAAGGGCCTGGTGTACATCCTAGGCCAGGAGTCCCTCTGTTTATCTACAACGAGGAGCT
GGTGAGCATGAACGTGCAGGTTGATTATGAGCCAATCGATGCCACCAGTTTCATCAACATCAATTCCCTCAGGCTGAAGG
AATATCATCATCTCCAGAGCAAGGTCACTGCCAAA

Alignment

ORF - retro_ptro_3158 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 85.96 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 4
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MSSKGSVVLAYSGGLDTSCILVWLKEQGYDVIAYLANIGQKEDFEEARKKALKLGAKKVFIEDVSKEFVE
          MSSKGSVVLAYSGGLDTSCILV.LKEQGYD.IAY..N.GQKEDFEEARKKALKLG.KKVFIE.VSKEFV.
Retrocopy MSSKGSVVLAYSGGLDTSCILVLLKEQGYDIIAYVNNTGQKEDFEEARKKALKLGGKKVFIEEVSKEFVK

Parental  EFIWPAIQSSALYEDRYLLGTSLARPCIARKQVEIAQREGAKYVSHGATGKGNDQVRFELSCYSLAPHIK
          EFIW.AIQSSALYEDRYLLGTSL.RPCIARKQVEIAQ.E.AK.VSHGATGKGNDQV.FEL.CYSLAP.IK
Retrocopy EFIWLAIQSSALYEDRYLLGTSLTRPCIARKQVEIAQQERAK*VSHGATGKGNDQVQFELNCYSLAPQIK

Parental  VIAPWRMPEFYNRFKGRNDLMEYAKQHGIPIPVTPKNPWSMDENLMHISYEAGILENPKNQAPPGLYTKT
          VIAPWRMP.FYNRFK.RNDLME..KQHGIPIPVTPKNPWSMDENLM.IS.EAGILENPKNQA.PGL.TKT
Retrocopy VIAPWRMPKFYNRFKVRNDLMEHTKQHGIPIPVTPKNPWSMDENLMQISNEAGILENPKNQAFPGLSTKT

Parental  QDPAKAPNTPDILEIEFKKGVPVKVTNVKDGTTHQTSLELFMYLNEVAGKHGVGRIDIVENRFIGMKSRG
          QDPAKAP.TPDILEIEFK.GVPVKVTNVKDGTTHQTSLELF.Y..E.AGK...GRIDI.EN.F.GMKS.G
Retrocopy QDPAKAPRTPDILEIEFK*GVPVKVTNVKDGTTHQTSLELFLYISEDAGKYSLGRIDIKENHFTGMKSPG

Parental  IYETPAGTILYHAHLDIEAFTMDREVRKIKQGLGLKFAELVYTGFWHSPECEFVRHCIAKSQERVEGKVQ
          IYETPA.TI.YHAHLDI.AFTMDREV.KIK.GLGLKFAELVY.GFWHS.EC.FV.HCI.KSQE.VEGKVQ
Retrocopy IYETPADTIVYHAHLDIRAFTMDREVCKIK*GLGLKFAELVYSGFWHSLECKFVHHCITKSQE*VEGKVQ

Parental  VSVLKGQVYILGRES-PLSLYNEELVSMNVQGDYEPTDATGFININSLRLKEYHRLQSKVTAK
          VSV.KG.VYILG.ES.PL..YNEELVSMNVQ.DYEP.DAT.FININSLRLKEYH.LQSKVTAK
Retrocopy VSVFKGLVYILGQES<PLFIYNEELVSMNVQVDYEPIDATSFININSLRLKEYHHLQSKVTAK

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	42.11 RPM
SRP007412_cerebellum	0.04 RPM	48.83 RPM
SRP007412_heart	0.03 RPM	16.26 RPM
SRP007412_kidney	0.21 RPM	1168.07 RPM
SRP007412_liver	0.13 RPM	933.12 RPM
SRP007412_testis	0.00 RPM	18.44 RPM

ChIP-Seq

Pan troglodytes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ptro_3158 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_3158 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_3158 has 1 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_4743

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Parental genes homology:

Parental genes homology involve 8 parental genes, and 68 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000020554	3 retrocopies	retro_cjac_1219, retro_cjac_4038, retro_cjac_4209,
Homo sapiens	ENSG00000130707	14 retrocopies	retro_hsap_2247, retro_hsap_2885, retro_hsap_3109, retro_hsap_3175, retro_hsap_3252, retro_hsap_3564, retro_hsap_3824, retro_hsap_4149, retro_hsap_4182, retro_hsap_4648, retro_hsap_4743, retro_hsap_4934, retro_hsap_820, retro_hsap_985,
Gorilla gorilla	ENSGGOG00000010228	8 retrocopies	retro_ggor_1346, retro_ggor_1675, retro_ggor_2134, retro_ggor_2403, retro_ggor_2574, retro_ggor_2787, retro_ggor_671, retro_ggor_787,
Myotis lucifugus	ENSMLUG00000006066	2 retrocopies	retro_mluc_1058, retro_mluc_1304,
Mus musculus	ENSMUSG00000076441	1 retrocopy	retro_mmus_135,
Nomascus leucogenys	ENSNLEG00000012500	13 retrocopies	retro_nleu_1088, retro_nleu_1245, retro_nleu_1317, retro_nleu_1381, retro_nleu_1390, retro_nleu_1424, retro_nleu_1701, retro_nleu_1792, retro_nleu_220, retro_nleu_253, retro_nleu_2680, retro_nleu_2764, retro_nleu_625,
Pongo abelii	ENSPPYG00000019692	13 retrocopies	retro_pabe_1963, retro_pabe_2390, retro_pabe_2637, retro_pabe_2696, retro_pabe_2937, retro_pabe_3069, retro_pabe_3197, retro_pabe_3422, retro_pabe_3460, retro_pabe_3521, retro_pabe_3522, retro_pabe_731, retro_pabe_834,
Pan troglodytes	ENSPTRG00000021473	14 retrocopies	retro_ptro_1590, retro_ptro_1951, retro_ptro_2101, retro_ptro_2199, retro_ptro_2268, retro_ptro_2421, retro_ptro_2602, retro_ptro_2821, retro_ptro_2836, retro_ptro_3064, retro_ptro_3158 , retro_ptro_3298, retro_ptro_571, retro_ptro_762,