RetrogeneDB ID: retro_ggor_1148

Retrocopy location

• Organism: Gorilla (Gorilla gorilla)
• Coordinates: 15:29273747..29275052(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: AHCY
• Ensembl ID: ENSGGOG00000014694
• Aliases: None
• Description: Adenosylhomocysteinase [Source:UniProtKB/TrEMBL;Acc:G3SA81]

Sequence

>retro_ggor_1148
ATGTCTCATTAACTACTCTACGAGGTTGCTGACATTGGTTTGGCCGCCTGGGGATGCAAGGCCTTGGACACTGAGGAGAA
CAAGAAGCCAGGCCTGATGCACGTGTAGGAGCTGTACTCAGCCTCCAAGCCACTGAAGAGCGTCCGCATCAGCGGCTGCC
TGCACATGACTGTGGAGACAGTCGTCCTCACTGAGACCCTCCTTGTCCTGGGTGCTGAAGTGCAGTGGTCCAGCTGCAAC
ATCTTCTCCACCCAGGACCATGCAGCAGCTGCCATTGCCAAGGCTGGGATTCCAGTGAACGCCTGGAAGGGAGAAACGGA
GAAGTACCTTTGGTGCACCAAGCAGACACTGTACTTCAAGGACAAGCTCCTCAACATGATTCTGGACATCACTGGGGGCC
TCACCAACCTCACCCACACTAAGTACCCACAGCTCTTGTCGGGCATCAGAGACATCTCCGAGGAGACCATGACTGAGGTC
CACAACCTATACAAGATGATGGCCAATGGGATCCTGAAGGTGTCCACCATCAACGTTAATGATTCTGTCATCAAGAGCAA
GTTTGACAACCTCTATGGCTGCCACCAGTCCCTCCCCAGATGGCATCAAGTAGGCCATAGGTGTGATGATTGCCAGCAAG
GTAGCTGTGGTAGCGGCTATGGTGATGTGGGCAAGGGCTGTGCCCAGGCCCTGCAGGGTTTTGGGGCTCACGTCATTATC
ACCGAGATCGACCCCATCAATGCACTGCAGGCTGCCATGCAGGGCTATGAGGGGACCACCATGGACAAGGCCTGTCATGA
GGGCAACGTCTTTGTCACCACCACAGGCTGTGTTGACATCATCCTTGGCTAGCTGCCCAACAGGCACTTTGAACAGATGA
AGGATGATGCCATCGTGTGTAACACTGGACACTTTGACATGAAAATCAATGTCACGTGGCTCAACAAGAATGCTATGAAG
AAGGTGAACATCAAGCCCCAGATGGACTAGTACTGGCTAAAGAATGGGCGTGGCACCATCCTGCTGGCTGAGTGTCAGCT
GGTCTACCTGGGTTGTGCTATGGACCAACCCAGCTTTGTGATGAGTAACTCCTTCACCAACCATGTGATGGTGTAGATTG
AGCTGTGGACCCACTCAGACAAGTACCCCATTGAGGTTCACTTCCTGCCCAGGAAGCTGGATGAGGCAGTGGCTGAAGCC
CATCTGGGCAAGGTGAACATGAAACTGACCAAGCAGACTGAGAAGCAGGCCCAGTACCTGGGCATGTCCTGTGATAGTCT
CTTCAAGCTGGATCACTACCACTAC

Alignment

ORF - retro_ggor_1148 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 79.22 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 6
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

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

Parental  GAEVQWSSCNIFSTQDHAAAAIAKAGIPVYAWKGETDEEYLWCIEQTLYFKDGPLNMILDDGGDLTNLIH
          GAEVQWSSCNIFSTQDHAAAAIAKAGIPV.AWKGET.E.YLWC..QTLYFKD..LNMILD..G.LTNL.H
Retrocopy GAEVQWSSCNIFSTQDHAAAAIAKAGIPVNAWKGET-EKYLWCTKQTLYFKDKLLNMILDITGGLTNLTH

Parental  TKYPQLLPGIRGISEETTTGVHNLYKMMANGILKVPAINVNDSVTKSKFDNLYGCRESLI-DGIKRATDV
          TKYPQLL.GIR.ISEET.T.VHNLYKMMANGILKV..INVNDSV.KSKFDNLYGC..SL..DGIK.A..V
Retrocopy TKYPQLLSGIRDISEETMTEVHNLYKMMANGILKVSTINVNDSVIKSKFDNLYGCHQSLP>DGIK*AIGV

Parental  MIAGKVAVVA-GYGDVGKGCAQALRGFGARVIITEIDPINALQAAMEGYEVTTMDEACQEGNIFVTTTGC
          MIA.KVAVVA.GYGDVGKGCAQAL.GFGA.VIITEIDPINALQAAM.GYE.TTMD.AC.EGN.FVTTTGC
Retrocopy MIASKVAVVA<GYGDVGKGCAQALQGFGAHVIITEIDPINALQAAMQGYEGTTMDKACHEGNVFVTTTGC

Parental  IDIILG----RHFEQMKDDAIVCNIGHFDVEIDVKWLNENAVEKVNIKPQVDRYRLKNGRRIILLAEGRL
          .DIILG....RHFEQMKDDAIVCN.GHFD..I.V.WLN.NA..KVNIKPQ.D.Y.LKNGR..ILLAE..L
Retrocopy VDIILG*LPNRHFEQMKDDAIVCNTGHFDMKINVTWLNKNAMKKVNIKPQMD*YWLKNGRGTILLAECQL

Parental  VNLGCAMGHPSFVMSNSFTNQVMAQIELWTHPDKYPVGVHFLPKKLDEAVAEAHLGKLNVKLTKLTEKQA
          V.LGCAM..PSFVMSNSFTN.VM..IELWTH.DKYP..VHFLP.KLDEAVAEAHLGK.N.KLTK.TEKQA
Retrocopy VYLGCAMDQPSFVMSNSFTNHVMV*IELWTHSDKYPIEVHFLPRKLDEAVAEAHLGKVNMKLTKQTEKQA

Parental  QYLGMSCDGPFKPDHYRY
          QYLGMSCD..FK.DHY.Y
Retrocopy QYLGMSCDSLFKLDHYHY

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	26.18 RPM
SRP007412_cerebellum	0.00 RPM	11.78 RPM
SRP007412_heart	0.00 RPM	18.01 RPM
SRP007412_kidney	0.08 RPM	180.85 RPM
SRP007412_liver	0.03 RPM	97.10 RPM
SRP007412_testis	0.10 RPM	56.05 RPM

ChIP-Seq

Gorilla gorilla was not studied using ChIP-Seq data.

EST

Gorilla gorilla was not studied using EST data.

TSS

Gorilla gorilla was not studied using FANTOM5 data.

Lab

retro_ggor_1148 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ggor_1148 has 3 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_1496
Pan troglodytes	retro_ptro_1015
Pongo abelii	retro_pabe_1247

---

Parental genes homology:

Parental genes homology involve 18 parental genes, and 61 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000018101	1 retrocopy	retro_btau_1140,
Canis familiaris	ENSCAFG00000007504	2 retrocopies	retro_cfam_1486, retro_cfam_552,
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,
Otolemur garnettii	ENSOGAG00000016787	3 retrocopies	retro_ogar_3223, retro_ogar_3401, retro_ogar_3402,
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,