RetrogeneDB ID: retro_pabe_2108

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: 2b:27916309..27917305(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: AHCY
• Ensembl ID: ENSPPYG00000010935
• Aliases: None
• Description: adenosylhomocysteinase [Source:HGNC Symbol;Acc:343]

Sequence

>retro_pabe_2108
CATGCCTGGAAGGGCAAAACAGACGAGGAGTACCTGTGGCGCATTGAGCAGATGATGTACTTCAAGGACGGGCCCCTCAA
CATGATTCTGGAAGACAGGGGCGACCTCAACAACCTCATCCACACCGAGTACCCGCAGCTCCTGCCGAGCTTCCGAGGTA
TATCCGAAGAGACCACGATCGGGGTCCACAACCTGTACAAGATGATGGCCAATGGGATCCTGAAAGTGCCTGCCATTGAT
GTCAATGACTCTGCCACCAAGAGCAAGTTTGACAACCTATGGCTGTGGGAGCCCCTCATAGATGGTATCAAGCAGGCCAC
AGACGTGATGATTGCCAGCAAGGTAGTGGTGGTAGCAGGCTATGGCGATGTGGGCAACAGCTGTGCCCAGGCCCTGCGGG
GTTTCAGGGCCAGCATCATCATCACCAAGATTGACCCCATCAAGTCACTGCAAGCTGCCATGGAGGGCTATGAGATGACT
ACCATGGATGAGGCCTGTCAGGAGGGCCACGTCTTTGTCACCACCACAGGTTGTGTTGACATCATCCTTGGCCAGCACTT
TGAGGAGATGAAGGATGATGCCATTGTATGTAACACTGGATACTTTGATGTGGAGATGGATGTCAAGTGGCTCAACAAGA
ACACTGTGGAGAAGGTGAACATCAAGCTGCAGGTGAACCCGTACCGGCTGAAAAATGGGCGCTGCACCATCCTGCTGGCT
GAGGGTTGGCTGGTTAACCTGGCTTGTGCCATCGGTCACCCCAGCTTCGTGATGAGTAACTCCTTCACCAGCCAGGTGAT
AGCGCAGATCCAGCTGCGGACCCACCCAGACAAGTACACTGTTAGGGTTCACTTCCTGCCCAAGAAGCTGGATGAGTCAG
TGGCTGAAGCCCACCTGGGAGAGCTGAACATGAAGTTGACCAAGCTGACTGAGAAGCAGGCCCAGTACCTGGGCATGTCT
TGTTACTGCCCCTTCAAGCCAGATCACTACCACTAC

Alignment

ORF - retro_pabe_2108 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 81.68 %
• Parental protein coverage: 77.08 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  YAWKGETDEEYLWCIEQTLYFKDGPLNMILDDGGDLTNLIHTKYPQLLPGIRGISEETTTGVHNLYKMMA
          .AWKG.TDEEYLW.IEQ..YFKDGPLNMIL.D.GDL.NLIHT.YPQLLP..RGISEETT.GVHNLYKMMA
Retrocopy HAWKGKTDEEYLWRIEQMMYFKDGPLNMILEDRGDLNNLIHTEYPQLLPSFRGISEETTIGVHNLYKMMA

Parental  NGILKVPAINVNDSVTKSKFDNLYGCRESLIDGIKRATDVMIAGKVAVVAGYGDVGKGCAQALRGFGARV
          NGILKVPAI.VNDS.TKSKFDNL....E.LIDGIK.ATDVMIA.KV.VVAGYGDVG..CAQALRGF.A..
Retrocopy NGILKVPAIDVNDSATKSKFDNLW-LWEPLIDGIKQATDVMIASKVVVVAGYGDVGNSCAQALRGFRASI

Parental  IITEIDPINALQAAMEGYEVTTMDEACQEGTIFVTTTGCVDIILGRHFEQMKDDAIVCNIGHFDVEIDVK
          IIT.IDPI..LQAAMEGYE.TTMDEACQEG..FVTTTGCVDIILG.HFE.MKDDAIVCN.G.FDVE.DVK
Retrocopy IITKIDPIKSLQAAMEGYEMTTMDEACQEGHVFVTTTGCVDIILGQHFEEMKDDAIVCNTGYFDVEMDVK

Parental  WLNENAVEKVNIKPQVDRYRLKNGRRIILLAEGRLVNLGCAMGHPSFVMSNSFTNQVMAQIELWTHPDKY
          WLN.N.VEKVNIK.QV..YRLKNGR..ILLAEG.LVNL.CA.GHPSFVMSNSFT.QV.AQI.L.THPDKY
Retrocopy WLNKNTVEKVNIKLQVNPYRLKNGRCTILLAEGWLVNLACAIGHPSFVMSNSFTSQVIAQIQLRTHPDKY

Parental  PVGVHFLPKKLDEAVAEAHLGKLNVKLTKLTEKQAQYLGMSRDGPFKPDHYRY
          .V.VHFLPKKLDE.VAEAHLG.LN.KLTKLTEKQAQYLGMS...PFKPDHY.Y
Retrocopy TVRVHFLPKKLDESVAEAHLGELNMKLTKLTEKQAQYLGMSCYCPFKPDHYHY

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	31.63 RPM
SRP007412_cerebellum	0.00 RPM	24.69 RPM
SRP007412_heart	0.00 RPM	19.27 RPM
SRP007412_kidney	0.00 RPM	184.63 RPM
SRP007412_liver	0.00 RPM	64.75 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_2108 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_2108 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_2108 has 2 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_2325
Pan troglodytes	retro_ptro_1698

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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,