RetrogeneDB ID: retro_ptro_1015

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: 15:47634214..47635523(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: AHCY
• Ensembl ID: ENSPTRG00000013414
• Aliases: None
• Description: Adenosylhomocysteinase [Source:UniProtKB/TrEMBL;Acc:H2QK78]

Sequence

>retro_ptro_1015
ATGTCTCATTAACTACTCTACGAGGTTGCTGACATTGGTTTGGCCGCCTGGGGATGCAAGGCCCTGGACACTGAGGAGAA
CAAGAAGCCAGGCCTGATGCACGTGTAGGAGCTGTACTCAGCCTCCAAGCCACTGAAGAGCGTCCGCATCACTGGCTGCC
TGCACATGACTGTGGAGACAGTCATCCTCACTGAGACCCTCCTTGTCCTGGGTGCTGAAGTGCAGTGGTCCAGCTGCAAC
ATCTTCTCCACCCAGGACCATGCAGCAGCTGCCATTGCCAAGGCTGGGATTCCAGTGAACGCCTGGAAGGGAGAAACGGA
GGAGAAGTACCTTTGGTGCACCAAGCAGACACTGTACTTCAAGGACAAGCTCCTCAACATGATTCTGGACATCACTGGGG
GCCTCACCAACCTCACCCACACTAAGTACCCACAGCTCTTGTTGGGCATCAGAGACATCTCCGAGGAGACCATGACTGAG
GTCCACAACCTATACAAGATGATGGCCAATGGGATCCTGAAGGTGTCCACCATCAACGTTAATGATTCTGTCACCAAGAG
CAAGTTTGACAACCTCTATGGCTGCCACCAGTCCCTCCCCAGATGGCATCAAGTAGGCCATAGGTGTGATGATTGCCAGC
AAGGTAGCTGTGGTAGCGGGCTATGGTGATGTGGGCAAGGGCTGTGCCCAGGCCCTGCAGGGATTCGGGGCTCACGTCAT
TATCACCGAGATCGACCCCATCAATGCACTGCAGGCTGCCATGCAGCGCTATGAGGGGACCACCATGGACAAGGCCTGTC
AGGAGGGCAACATCTTTGTCACCACCACAGGCTGTGTTGACATCATCCTTGGCTAGCTGCCCAACAGGCACTTTGAACAG
ATGAAGGATGATGCCATCGTGTGTAACACTGGACACTTTGACGTGAAAATAGATGTCAGGTGGCTCAACAAGAATGCTAT
GAAGAAGGTGAACATCAAGCCCCAGATGGACTAGTACTGGCTAAAGAATGGGCGTGGCACCATCCTGCTGGCTGAGTGTC
AGCTGGTCTACCTGGGTTGTGCTATGGACCAACCCAGCTTTGTGATGAGTAACTCCTTCACCAACCATGTGATGGTGCAG
ATTGAGCTGTGGACCCACTCAGATAAGTACCCCATTGAGGTTCACTTCCTGCCCAGGAAGCTGGATGAGGCAGTGGCTGA
AGCCCATCTGGGCAAGGTGAACATGAAACTGACCAAGCAGACTGAGAAGCAGGCCCAGTACCTGGGCATGTCCTGTGATA
GTCTCTTCAAGCTGGATCACTACCACTAC

Alignment

ORF - retro_ptro_1015 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 80.32 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 5
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MSDKLPYKVADIGLAAWGRKALDIAENEMPGLMRMRERYSASKPLKGARIAGCLHMTVETAVLIETLVTL
          MS..L.Y.VADIGLAAWG.KALD..EN..PGLM...E.YSASKPLK..RI.GCLHMTVET..L.ETL..L
Retrocopy MSH*LLYEVADIGLAAWGCKALDTEENKKPGLMHV*ELYSASKPLKSVRITGCLHMTVETVILTETLLVL

Parental  GAEVQWSSCNIFSTQDHAAAAIAKAGIPVYAWKGETDEEYLWCIEQTLYFKDGPLNMILDDGGDLTNLIH
          GAEVQWSSCNIFSTQDHAAAAIAKAGIPV.AWKGET.E.YLWC..QTLYFKD..LNMILD..G.LTNL.H
Retrocopy GAEVQWSSCNIFSTQDHAAAAIAKAGIPVNAWKGETEEKYLWCTKQTLYFKDKLLNMILDITGGLTNLTH

Parental  TKYPQLLPGIRGISEETTTGVHNLYKMMANGILKVPAINVNDSVTKSKFDNLYGCRESL-IDGIKRATDV
          TKYPQLL.GIR.ISEET.T.VHNLYKMMANGILKV..INVNDSVTKSKFDNLYGC..SL..DGIK.A..V
Retrocopy TKYPQLLLGIRDISEETMTEVHNLYKMMANGILKVSTINVNDSVTKSKFDNLYGCHQSL>PDGIK*AIGV

Parental  MIAGKVAVVAGYGDVGKGCAQALRGFGARVIITEIDPINALQAAMEGYEVTTMDEACQEGNIFVTTTGCI
          MIA.KVAVVAGYGDVGKGCAQAL.GFGA.VIITEIDPINALQAAM..YE.TTMD.ACQEGNIFVTTTGC.
Retrocopy MIASKVAVVAGYGDVGKGCAQALQGFGAHVIITEIDPINALQAAMQRYEGTTMDKACQEGNIFVTTTGCV

Parental  DIILG----RHFEQMKDDAIVCNIGHFDVEIDVKWLNENAVEKVNIKPQVDRYRLKNGRRIILLAEGRLV
          DIILG....RHFEQMKDDAIVCN.GHFDV.IDV.WLN.NA..KVNIKPQ.D.Y.LKNGR..ILLAE..LV
Retrocopy DIILG*LPNRHFEQMKDDAIVCNTGHFDVKIDVRWLNKNAMKKVNIKPQMD*YWLKNGRGTILLAECQLV

Parental  NLGCAMGHPSFVMSNSFTNQVMAQIELWTHPDKYPVGVHFLPKKLDEAVAEAHLGKLNVKLTKLTEKQAQ
          .LGCAM..PSFVMSNSFTN.VM.QIELWTH.DKYP..VHFLP.KLDEAVAEAHLGK.N.KLTK.TEKQAQ
Retrocopy YLGCAMDQPSFVMSNSFTNHVMVQIELWTHSDKYPIEVHFLPRKLDEAVAEAHLGKVNMKLTKQTEKQAQ

Parental  YLGMSCDGPFKPDHYRY
          YLGMSCD..FK.DHY.Y
Retrocopy YLGMSCDSLFKLDHYHY

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	0.05 RPM	36.75 RPM
SRP007412_cerebellum	0.00 RPM	19.04 RPM
SRP007412_heart	0.00 RPM	25.94 RPM
SRP007412_kidney	0.05 RPM	149.14 RPM
SRP007412_liver	0.00 RPM	107.07 RPM
SRP007412_testis	0.00 RPM	149.75 RPM

ChIP-Seq

Pan troglodytes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ptro_1015 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_1015 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_1015 has 3 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_1496
Gorilla gorilla	retro_ggor_1148
Pongo abelii	retro_pabe_1247

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Parental genes homology:

Parental genes homology involve 15 parental genes, and 55 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000018303	7 retrocopies	retro_cjac_1028, retro_cjac_1248, retro_cjac_1806, retro_cjac_2132, retro_cjac_2839, retro_cjac_3287, retro_cjac_480,
Echinops telfairi	ENSETEG00000002576	1 retrocopy	retro_etel_444,
Homo sapiens	ENSG00000101444	6 retrocopies	retro_hsap_1496, retro_hsap_2325, retro_hsap_2365, retro_hsap_4213, retro_hsap_571, retro_hsap_803,
Gorilla gorilla	ENSGGOG00000014694	5 retrocopies	retro_ggor_1148, retro_ggor_1795, retro_ggor_2822, retro_ggor_3087, retro_ggor_511,
Monodelphis domestica	ENSMODG00000002753	1 retrocopy	retro_mdom_1974,
Mus musculus	ENSMUSG00000027597	1 retrocopy	retro_mmus_197,
Nomascus leucogenys	ENSNLEG00000010041	4 retrocopies	retro_nleu_1717, retro_nleu_2785, retro_nleu_40, retro_nleu_929,
Oryctolagus cuniculus	ENSOCUG00000008592	1 retrocopy	retro_ocun_1886,
Pongo abelii	ENSPPYG00000010935	9 retrocopies	retro_pabe_1247, retro_pabe_1978, retro_pabe_2108, retro_pabe_2189, retro_pabe_3446, retro_pabe_647, retro_pabe_658, retro_pabe_665, retro_pabe_718,
Pan troglodytes	ENSPTRG00000013414	7 retrocopies	retro_ptro_1015 , retro_ptro_1698, retro_ptro_1730, retro_ptro_2860, retro_ptro_3011, retro_ptro_559, retro_ptro_771,
Rattus norvegicus	ENSRNOG00000017777	7 retrocopies	retro_rnor_1142, retro_rnor_1820, retro_rnor_1903, retro_rnor_2120, retro_rnor_569, retro_rnor_647, retro_rnor_839,
Sus scrofa	ENSSSCG00000007278	1 retrocopy	retro_sscr_119,
Tarsius syrichta	ENSTSYG00000007163	3 retrocopies	retro_tsyr_1178, retro_tsyr_1529, retro_tsyr_1582,
Tursiops truncatus	ENSTTRG00000003632	1 retrocopy	retro_ttru_1666,
Xenopus tropicalis	ENSXETG00000019486	1 retrocopy	retro_xtro_62,