RetrogeneDB ID: retro_ptro_559

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: 11:83775442..83776734(+)
• Located in intron of: ENSPTRG00000004139

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_559
ATGTCTGACAAACTGCCCTACAAAGTCACTGACATTGGCCTGGACTTCTGGGGACGCAAAGCCCTGGATATTGTGGAGAA
CCAGATGCCGGGCCTGACGTGCATGTGGGAGCTGTACTCGACCCTCCAAGCCCTTGAAGGGCACGCGCATCACCAGTTGC
CTCCATAGGACCCATGGAGATGGCCATCCTCATTGAGACCCTCATTACCCTGGGTGCCAAGCTGCAGTGGTCCAGCTGCA
ACATCACCCAGGACCATGCGGCAGCTGCCACTGCCAAGGCTGGCATTCCAGTTGTACGCCTGGAAGGGCGAAACAGAGGA
AGAGTACCTGTGGTGCACCAAGCAGATATTATACTTCAAAGACGGCCTCCTCAACGTGATTCTGGATGTCGCTGGGGCCC
CCACCAACCTCATCCACACCAAGTACCCACAGCTCTTGTCGGGGATGTGAGGCATCTTCAAGGAGACCATGATTGGGGTC
CACAAGCTACACAAGATGATGGCCAATGGGATCCTGAAAGTGCCTGCCATCAATGTCAACAACTCCGTCACCAAGAGCAA
GTTTGACAACCTCTCCGGCTGCCAGGAGTCCCTCATAGATAGCATCAAGTGGGCCACAGACGCGATGATTGCCAGCAAGG
TAGCAGTGGTAGCAGGCTGTGGCAACATGGGCAAAGGCTGTGCCCAGGCCCTGTGGGGTTTCAGGCCCATGTCATCATCA
TCAAGATCGACCCCATCAACATACTGCAGGCTGCCATGAAGGGCTATGAGATGGCCACCATAGACGAGGCCTGTCAGGAG
GACAACATCTTTGTCACCACCACAGGCTGTGTTAACATCATCCTTGGCTGGCACTTTAAGCAGATGAAGGATGATGCCAT
CATTTGTAACACTGGACACTTTGACATGGAGATTGATGTCAAGTGGCTCAACAAGAATACTGTGGAGAGAGTCAACATCA
AGCCCCAGGTGGACTGGTATCAGCTGAAGAATGCACACCACATCATCCTGCTAGCTGAGGGTCAGCTGGTCAACCTGGGT
TGTGCCATGGGCCACCTCAGCTTCTTGATAAGTAACTCCTTCACCAACCAAGTGATGGCGCAGACTGAGCTGCAGACCCA
CCCAGACAAGTACCAGGTTATGGTTCTCTTCCTGCCCAAGAAGCTGAATGAGGCAATGGCTGAAGCCCACCTGGGCAAGC
TGAATGTGAAATTGACCAAGCTGACTGAGCTGCAAGCCCATTACCTGTACTTGTCCCGTGATGGCCCCTTCAAGCCAGAT
CACTACCACTAC

Alignment

ORF - retro_ptro_559 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 77.29 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 1
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  MSDKLPYKVADIGLAAWGRKALDIAENEMPGLMRMRERYSA-SKPLKGARIAGCLHMT-VETAVLIETLV
          MSDKLPYKV.DIGL..WGRKALDI.EN.MPGL..M.E.YS..SKPLKG.RI..CLH.T..E.A.LIETL.
Retrocopy MSDKLPYKVTDIGLDFWGRKALDIVENQMPGLTCMWELYST>SKPLKGTRITSCLHRT>MEMAILIETLI

Parental  TLGAEVQWSSCNIFSTQDHAAAAIAKAGIPV-YAWKGETDEEYLWCIEQTLYFKDGPLNMILDDGGDLTN
          TLGA..QWSSCNI..TQDHAAAA.AKAGIPV.YAWKGET.EEYLWC..Q.LYFKDG.LN.ILD..G..TN
Retrocopy TLGAKLQWSSCNI--TQDHAAAATAKAGIPV>YAWKGETEEEYLWCTKQILYFKDGLLNVILDVAGAPTN

Parental  LIHTKYPQLLPGIRGISEETTTGVHNLYKMMANGILKVPAINVNDSVTKSKFDNLYGCRESLIDGIKRAT
          LIHTKYPQLL.G..GI..ET..GVH.L.KMMANGILKVPAINVN.SVTKSKFDNL.GC.ESLID.IK.AT
Retrocopy LIHTKYPQLLSGM*GIFKETMIGVHKLHKMMANGILKVPAINVNNSVTKSKFDNLSGCQESLIDSIKWAT

Parental  DVMIAGKVAVVAGYGDVGKGCAQALRGFG-ARVIITEIDPINALQAAMEGYEVTTMDEACQEGNIFVTTT
          D.MIA.KVAVVAG.G..GKGCAQAL.GF..A.VII..IDPIN.LQAAM.GYE..T.DEACQE.NIFVTTT
Retrocopy DAMIASKVAVVAGCGNMGKGCAQALWGFR<AHVIIIKIDPINILQAAMKGYEMATIDEACQEDNIFVTTT

Parental  GCIDIILGRHFEQMKDDAIVCNIGHFDVEIDVKWLNENAVEKVNIKPQVDRYRLKNGRRIILLAEGRLVN
          GC..IILG.HF.QMKDDAI.CN.GHFD.EIDVKWLN.N.VE.VNIKPQVD.Y.LKN...IILLAEG.LVN
Retrocopy GCVNIILGWHFKQMKDDAIICNTGHFDMEIDVKWLNKNTVERVNIKPQVDWYQLKNAHHIILLAEGQLVN

Parental  LGCAMGHPSFVMSNSFTNQVMAQIELWTHPDKYPVGVHFLPKKLDEAVAEAHLGKLNVKLTKLTEKQAQY
          LGCAMGH.SF..SNSFTNQVMAQ.EL.THPDKY.V.V.FLPKKL.EA.AEAHLGKLNVKLTKLTE.QA.Y
Retrocopy LGCAMGHLSFLISNSFTNQVMAQTELQTHPDKYQVMVLFLPKKLNEAMAEAHLGKLNVKLTKLTELQAHY

Parental  LGMSCDGPFKPDHYRY
          L..S.DGPFKPDHY.Y
Retrocopy LYLSRDGPFKPDHYHY

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	36.75 RPM
SRP007412_cerebellum	0.00 RPM	19.04 RPM
SRP007412_heart	0.00 RPM	25.94 RPM
SRP007412_kidney	0.00 RPM	149.14 RPM
SRP007412_liver	0.00 RPM	107.07 RPM
SRP007412_testis	0.11 RPM	149.75 RPM

ChIP-Seq

Pan troglodytes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ptro_559 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_559 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_559 has 2 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_803
Pongo abelii	retro_pabe_718

---

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,