RetrogeneDB ID: retro_pabe_718

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: 11:81638498..81639712(+)
• Located in intron of: ENSPPYG00000003743

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_718
CAGATGCCGGGCCTGACATGCATGTGGGAGCTGTACTCGACCCTCCAAGCCCTTGAAGGGCACCCGCATCACCAGTTGCC
TCCACAGGACCCATGGAGATGGCCATCCTCATTGAGATCCTCATTACGCTGGGTGCCAAGCTGCAGTGGTCCAGCTGCAA
CATCACCCAGGACCATGCGGCAGCTGCCATTGCCAAGGCTGGCATTCCAGTTGTATGCCTGGAAGGGCGAAACAGAGGAG
AAGTACCTGTGGTGCACCAAGCGGACATTATACTTCAAAGACAGGCTCCTCAACGTGATTCTGGATGTCTCTGGGGCCCC
CACCAACCTCATCCACACCAAGTACCCACAGCTCTTGTCAGGGATGTGAGGCATCTTCAAGGAGACCGTTACTGGGGTCC
ACAAGCTACACAAGATGATGGCCAATGGGATCCTGAAAGTGCCTGCCATCAATGTCAACAACTCCGTCACCAAGAGCAAG
TTTGACAACCTCTCCAGCTGCCAGGAGTCCCTCATAGATGGCATCAAGTGGGCCACAGACGTGATGATTGCCAGCAAGGT
AGCAGTGGTAGCAGGCTGTGGAAACATGAGCAAAGGCTGTGCCCAGGCCCTGTGGGGTTTCAGGCCCATGTCATCATCAT
CAAGATTTTCGACCCCATCAACACACTGCAGGCTGCCATGAAGGGCTATGAGGTGGCCACCATAGACAAGGCCTGTCAGG
AGGACAACATCTTTGTCACCACCACAGGCTGTGTTAACATCATCCTTGGCTGGCACTTTAAGCAGATGAAGGATGATGCC
ATCATGTGTAACACTGGACACTTTGACATGGAGATTGATGTCAAGTGGCTCAACAAGAACACTGTGGAGAGAGTCAACAT
CAAGCTCCAGGTGGACTGGTATCAGCTGAAGCATGCACACCACATCATCCTGCTAGCTGAGGGTCAGCTGGTCAACCTGG
GTTGTGCCATGGGCCACCCCAGCTTCTTGATAAGTAACTCCTTCACCAACCAAGTGATGGCGCAGACTGAGCTGCGGACC
CACCCAGACAAGTACCAGGTTATGGTTCTCTTCCTGCCCAAGAAGCTGAATGAGGCAATAGCTGAAGCCCACCTGGGCAA
GCTGAATGTGAAATTGACCAAGCTGACTGAGCTGCAAGCCCATTACCTGTACTTGTCCCGTGATGGCCCCTTCAAGCCAG
ATCACTACCACTAC

Alignment

ORF - retro_pabe_718 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 76.34 %
• Parental protein coverage: 93.75 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  EMPGLMRMRERYSA-SKPLKGARIAGCLHMT-VETAVLIETLVTLGAEVQWSSCNIFSTQDHAAAAIAKA
          .MPGL..M.E.YS..SKPLKG.RI..CLH.T..E.A.LIE.L.TLGA..QWSSCNI..TQDHAAAAIAKA
Retrocopy QMPGLTCMWELYST>SKPLKGTRITSCLHRT>MEMAILIEILITLGAKLQWSSCNI--TQDHAAAAIAKA

Parental  GIPV-YAWKGETDEEYLWCIEQTLYFKDGPLNMILDDGGDLTNLIHTKYPQLLPGIRGISEETTTGVHNL
          GIPV.YAWKGET.E.YLWC...TLYFKD..LN.ILD..G..TNLIHTKYPQLL.G..GI..ET.TGVH.L
Retrocopy GIPV>YAWKGETEEKYLWCTKRTLYFKDRLLNVILDVSGAPTNLIHTKYPQLLSGM*GIFKETVTGVHKL

Parental  YKMMANGILKVPAINVNDSVTKSKFDNLYGCRESLIDGIKRATDVMIAGKVAVVAGYGDVGKGCAQALRG
          .KMMANGILKVPAINVN.SVTKSKFDNL..C.ESLIDGIK.ATDVMIA.KVAVVAG.G...KGCAQAL.G
Retrocopy HKMMANGILKVPAINVNNSVTKSKFDNLSSCQESLIDGIKWATDVMIASKVAVVAGCGNMSKGCAQALWG

Parental  FG-ARVIITEI-DPINALQAAMEGYEVTTMDEACQEGTIFVTTTGCVDIILGRHFEQMKDDAIVCNIGHF
          F..A.VII..I.DPIN.LQAAM.GYEV.T.D.ACQE..IFVTTTGCV.IILG.HF.QMKDDAI.CN.GHF
Retrocopy FR<AHVIIIKIFDPINTLQAAMKGYEVATIDKACQEDNIFVTTTGCVNIILGWHFKQMKDDAIMCNTGHF

Parental  DVEIDVKWLNENAVEKVNIKPQVDRYRLKNGRRIILLAEGRLVNLGCAMGHPSFVMSNSFTNQVMAQIEL
          D.EIDVKWLN.N.VE.VNIK.QVD.Y.LK....IILLAEG.LVNLGCAMGHPSF..SNSFTNQVMAQ.EL
Retrocopy DMEIDVKWLNKNTVERVNIKLQVDWYQLKHAHHIILLAEGQLVNLGCAMGHPSFLISNSFTNQVMAQTEL

Parental  WTHPDKYPVGVHFLPKKLDEAVAEAHLGKLNVKLTKLTEKQAQYLGMSRDGPFKPDHYRY
          .THPDKY.V.V.FLPKKL.EA.AEAHLGKLNVKLTKLTE.QA.YL..SRDGPFKPDHY.Y
Retrocopy RTHPDKYQVMVLFLPKKLNEAIAEAHLGKLNVKLTKLTELQAHYLYLSRDGPFKPDHYHY

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	0.06 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_718 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_718 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_718 has 2 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_803
Pan troglodytes	retro_ptro_559

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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,