RetrogeneDB ID: retro_ptro_1590

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: 2A:39382115..39383034(-)
• Located in intron of: ENSPTRG00000011853

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_1590
TCATCTGGCCTGTATGAGGACTGCTACCTCCTGGGCCCCTCTCTTCCCAGGCCTTACATCACCCGCAAACAAGTGGAAAT
TGCTCAGTGGGAGGGGGCAAAGTATGTGTCCCACAGTGCCATGGGAAAGGGGAACGATCAGGTCTGGTTTGAGCTCGCCT
GCTACTCGCTGGCCCCCCAGATTAAGGTCATTGCTCCTGGGAGGATCCCTGAGTTCTACAACCAGTCCAAGGGCCACAGT
GATCTGATGGAATATGCAGAGAAACATGGGATTCCCATCCCAGTCACTCTGAAGCACCCATGGAACATGGACGAGAACCT
CATGCACATCAGCCACGAGGCTGGAATCTTGGAGAACCCCAAGAACCAAGCACCTTCAGGTCTCTACATGAAGATTCAGG
ACCTGGCCAAAGCCCCCAACACCCCCAACATTTTCAAGACTGAGTAAAAAAGGGGTCCCTGTGAAGGTGACCAGCATCAA
GGATGGCACCACCCACCAGACCTCCTTGGTGCTCTTCATGTACCTGAATGAAGTCGCAGGCAAGCACAGCGTGGGCCATA
TTGACATCGTGGAGAACCGCTTCATTGAAATGAAGTCCTGAGGTATCTGCAAGACCCCAGCAGGCACCATCCTTTACCAC
CCTCATTTAGACATTGAGGGCTTTGCCATGGAACAGGAAGTGCGCAAAATCAAACAAGGCCTGGGCTTGAAATTTGCTGA
GTTGGTGTACACCGGTTTCTGGCACAACCCTCAGTGTGACTTTGCCCACCACTGCATTGCCAAGTCCCAGGACCGAGTGG
AAGGGAAAGTGCAGATATCCATCTTCAAGGGCCAGGTGTACATCCTCTGCCAGGAGCCCCCACTGTCTCTCTACAGTGGA
GAGCAGGTGAGCATGAACGTGCAGGGCAATGATGAGCCA

Alignment

ORF - retro_ptro_1590 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 77.6 %
• Parental protein coverage: 74.51 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  SSALYEDRYLLGTSLARPCIARKQVEIAQREGAKYVSHGATGKGNDQVRFELSCYSLAPHIKVIAPWRMP
          SS.LYED.YLLG.SL.RP.I.RKQVEIAQ.EGAKYVSH.A.GKGNDQV.FEL.CYSLAP.IKVIAP.R.P
Retrocopy SSGLYEDCYLLGPSLPRPYITRKQVEIAQWEGAKYVSHSAMGKGNDQVWFELACYSLAPQIKVIAPGRIP

Parental  EFYNRFKGRNDLMEYAKQHGIPIPVTPKNPWSMDENLMHISYEAGILENPKNQAPPGLYTKTQDPAKA-P
          EFYN..KG..DLMEYA..HGIPIPVT.K.PW.MDENLMHIS.EAGILENPKNQAP.GLY.K.QD.AKA.P
Retrocopy EFYNQSKGHSDLMEYAEKHGIPIPVTLKHPWNMDENLMHISHEAGILENPKNQAPSGLYMKIQDLAKA>P

Parental  NTPDILEIEFKKGVPVKVTNVKDGTTHQTSLELFMYLNEVAGKHGVGRIDIVENRFIGMKSRGIYETPAG
          ..P.......KKGVPVKVT..KDGTTHQTSL.LFMYLNEVAGKH.VG.IDIVENRFI.MKS.GI..TPAG
Retrocopy TPPTFSRLS-KKGVPVKVTSIKDGTTHQTSLVLFMYLNEVAGKHSVGHIDIVENRFIEMKS*GICKTPAG

Parental  TILYHAHLDIEAFTMDREVRKIKQGLGLKFAELVYTGFWHSPECEFVRHCIAKSQERVEGKVQVSVLKGQ
          TILYH.HLDIE.F.M..EVRKIKQGLGLKFAELVYTGFWH.P.C.F..HCIAKSQ.RVEGKVQ.S..KGQ
Retrocopy TILYHPHLDIEGFAMEQEVRKIKQGLGLKFAELVYTGFWHNPQCDFAHHCIAKSQDRVEGKVQISIFKGQ

Parental  VYILGRESPLSLYNEELVSMNVQGDYEP
          VYIL..E.PLSLY..E.VSMNVQG..EP
Retrocopy VYILCQEPPLSLYSGEQVSMNVQGNDEP

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	0.18 RPM	42.11 RPM
SRP007412_cerebellum	0.18 RPM	48.83 RPM
SRP007412_heart	0.09 RPM	16.26 RPM
SRP007412_kidney	0.29 RPM	1168.07 RPM
SRP007412_liver	1.28 RPM	933.12 RPM
SRP007412_testis	0.53 RPM	18.44 RPM

ChIP-Seq

Pan troglodytes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ptro_1590 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_1590 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_1590 has 4 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_2247
Gorilla gorilla	retro_ggor_1675
Pongo abelii	retro_pabe_1963
Callithrix jacchus	retro_cjac_1219

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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,