RetrogeneDB ID: retro_pabe_1978

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: 2a:12189091..12190377(-)
• 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_1978
ATGTCTGACAAACTGTCCTATAAAGTTGCTGACATCGACCTGGCCGCCTGGGGACACAAGGCCCTGGATATTGTGGAGAG
TGAGATGCTGGGTCTGATGCATGTGTGGGAGCTGTACTTCGCCTCCAAGCCACTGAAGGGCACCCATATCTCTGGCTGGC
CGTATGTGACCGTGGTGAGAGCCATCCTCACTGAGACCCGTTGTCTCCTTGGATGCTGAGGTACAGTGGTCCAGCCGCAA
CATCTTCTCCACCCAGGACCAGGTGGCGGCTGCCATTGCCAAGGCTGTCATTCCAGTGCATGCCTGGAAGGGTGAAACAA
GCAAGGGATACCTGTCATGCATCCAACAATCACTACTTCAAAGACATGCCCCTAAGCATTATTCTGGATGATGGTAGCGG
CCTCACCAACCACATCCACACCAAGTACCCATAGCTCTTGCCGGGCATCCAAGGCATCTCCGAGGAGACCACCACCGGGG
TCCACAACCTACGTAAGATTACGGCCAAGGGGATCCTGAAAGTGCCTGCCGTCAACAACTCCATCACCAAGAGCAACTTT
CACAGCCTCTAAGGCTGCCGGGAGTCCCTCATAGATGGCATCAAGAGGGCTACGGATGTGATGATTGTCGGCAAGGTAGC
CATGGTGGCAGGCTATGGCGACATGGGCAAGGGCTGTGCCCAGGCCCTGTGGAATTTTGGGGACCCCTTCATCATCACCA
AGATCGGCCCCATCAACCTGCTACAGACTGCCATGGAGGGCTATGAGGTGACCGCCGTAGATGAGGCCTGTCAGGAGGGC
AACATCTTTGTCACTGCCACAGGATGTGTTGACATCATCCTTGGCCAGCACTTTGAGCAGATGAAGGATGATGCGATCAT
GTGTAACCCTGGTCACTTTGACGTGGAGATCAATGCCAAGTGGCTCAACGTGAATGCTGGGGAGAAGGTGACCATCAAGC
CCCAGGTGGCCAGGACTGGCTGAAGAGCAGCACGGCACCATCCTGCTGGTTGAGGGTCTGCTGGTCAGCCTGGGCTGTTC
CATGTGCCACCTCGGCGTTGTGATGAGTGACTCCTTTACCAACCAGGTGATGGTGCAGATTGAGCTGTGGACCCACCCAG
ACAAGTACCCTGGTGGGATTTACTTGCTGCCCAAGAAGCTGAATGAGGCAGTGGCTGAATCCCACCTGGGCAAGCTGAAT
GTGAAACTCACAAGTTGACCAAGAAGCAGGCCCAGTACCTGGGTATGTCCTGTGGCAGCCCCTTCAAGCCAGATCACAAC
CGCTAC

Alignment

ORF - retro_pabe_1978 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 71.79 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 3
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  MSDKLPYKVADIGLAAWGRKALDIAENEMPGLMRMRERYSASKPLKGARIAGCLHMTVETAVLIET-LVT
          MSDKL.YKVADI.LAAWG.KALDI.E.EM.GLM...E.Y.ASKPLKG..I.G....TV..A.L.ET..V.
Retrocopy MSDKLSYKVADIDLAAWGHKALDIVESEMLGLMHVWELYFASKPLKGTHISGWPYVTVVRAILTET>VVS

Parental  LGAEVQWSSCNIFSTQDHAAAAIAKAGIPVYAWKGETDEEYLWCIEQTLYFKDGPLN-MILDDGGDLTNL
          L.AEVQWSS.NIFSTQD..AAAIAKA.IPV.AWKGET...YL.CI.Q.L.....P......D..G.LTN.
Retrocopy LDAEVQWSSRNIFSTQDQVAAAIAKAVIPVHAWKGETSKGYLSCIQQSLLQRHAPKH>ILDDGSG-LTNH

Parental  IHTKYPQLLPGIRGISEETTTGVHNLYKMMANGILKVPAINVNDSVTKSKFDNLYGCRESLIDGIKRATD
          IHTKYP.LLPGI.GISEETTTGVHNL.K..A.GILKVPA..VN.S.TKS.F..L.GCRESLIDGIKRATD
Retrocopy IHTKYP*LLPGIQGISEETTTGVHNLRKITAKGILKVPA--VNNSITKSNFHSL*GCRESLIDGIKRATD

Parental  VMIAGKVAVVAGYGDVGKGCAQALRGFGARVIITEIDPINALQAAMEGYEVTTMDEACQEGTIFVTTTGC
          VMI.GKVA.VAGYGD.GKGCAQAL..FG...IIT.I.PIN.LQ.AMEGYEVT..DEACQEG.IFVT.TGC
Retrocopy VMIVGKVAMVAGYGDMGKGCAQALWNFGDPFIITKIGPINLLQTAMEGYEVTAVDEACQEGNIFVTATGC

Parental  VDIILGRHFEQMKDDAIVCNIGHFDVEIDVKWLNENAVEKVNIKPQVDRYRLKNGRR-IILLAEGRLVNL
          VDIILG.HFEQMKDDAI.CN.GHFDVEI..KWLN.NA.EKV.IKPQV.R......R..I.L..EG.LV.L
Retrocopy VDIILGQHFEQMKDDAIMCNPGHFDVEINAKWLNVNAGEKVTIKPQVARTG*RAARH>ILLV-EGLLVSL

Parental  GCAMGHPSFVMSNSFTNQVMAQIELWTHPDKYPVGVHFLPKKLDEAVAEAHLGKLNVKLT-KLTEKQAQY
          GC.M.H...VMS.SFTNQVM.QIELWTHPDKYP.G...LPKKL.EAVAE.HLGKLNVKLT.KLT.KQAQY
Retrocopy GCSMCHLGVVMSDSFTNQVMVQIELWTHPDKYPGGIYLLPKKLNEAVAESHLGKLNVKLT<KLTKKQAQY

Parental  LGMSRDGPFKPDHYRY
          LGMS...PFKPDH.RY
Retrocopy LGMSCGSPFKPDHNRY

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	0.22 RPM	31.63 RPM
SRP007412_cerebellum	0.12 RPM	24.69 RPM
SRP007412_heart	0.00 RPM	19.27 RPM
SRP007412_kidney	0.27 RPM	184.63 RPM
SRP007412_liver	0.31 RPM	64.75 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_1978 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_1978 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_1978 has 1 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Callithrix jacchus	retro_cjac_1248

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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,