RetrogeneDB ID: retro_ptro_118

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: 9:38899004..38900558(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSPTRG00000020956
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: ALDH1A2
• Ensembl ID: ENSPTRG00000007113
• Aliases: None
• Description: aldehyde dehydrogenase 1 family, member A2 [Source:HGNC Symbol;Acc:15472]

Sequence

>retro_ptro_118
ATGCTGCGCTTCCTGGCACCCCGGCTGCTTAGCCTCCAGGGCAGGACTGCCCACTACTCCTCGGCAGCAGCCCTCCCAAG
CCCCATTCTGAACCCAGACATCCCCTACAACCAGCTGTTCATCAACAATGAATGGCAAGATGCAGTCAGCAAGAAGACCT
TCCCGACGGTCAACCCTACCACCGGGGAGGTCATCGGGCACGTGGCTGAAGGTGACCGGGCTGATGTGGATCGGGCCGTG
AAAGCAGCCCGGGAAGCCTTCCGCCTGGGGTCCCCATGGCGCCGGATGGATGCCTCTGAGCGGGGCCGGCTGCTGAACCG
CCTGGCAGACCTAGTGGAGCGGGATCGAGTCTACTTGGCCTCACTCGAGACCTTGGACAATGGGAAGCCTTTCCAAGAGT
CTTACGCCTTGGACTTGGATGAGGTCATCAAGGTGTATCGGTACTTTGCTGGCTGGGCTGACAAGTGGCATGGCAAGACC
ATCCCCATGGATGGCCAGCATTTCTGCTTCACCCGGCATGAGCCCGTTGGTGTCTGTGGCCAGATCATCCCGTGGAACTT
CCCCTTGGTCATGCAGGGTTGGAAACTTGCCCCAGCACTCGCCACAGGCAACACTGTGGTTATGAAGGTGGCAGAGCAGA
CCCCCCTCTCTGCCCTGTATTTGGCCTCCCTCATCAAGGAGGCAGGCTTTCCCCCTGGGGTGGTGAACATCATCACGGGC
TATGGCCCAACAGCAGGTGCGGCCATCGCCCAGCACATGGATGTTGACAAAGTTGCCTTCACCGGTTCCACCGAGGTGGG
CCACCTGATCCAGAAAGCAGCTGGCGATTCCAACCTCAAGAGAGTCACCCTGGAGCTGGGTGGTAAGAGCCCCAGCATCG
TGCTGGCCGATGCTGACATGGAGCATGCCGTGGAGCAGTGCCACGAAGCCCTGTTCTTCAACATGGGCCAGTGCTGCTGT
GCTGGCTCCCGGACCTTCGTGGAAGAATCCATCTACAATGAGTTTCTCGAGAGAACCGTGGAGAAAGCAAAGCAGAGGAA
AGTGGGGAACCCCTTTGAGCTGGACACCCAGCAGGGGCCTCAGGTGGACAAGGAGCAGTTTGAACGAGTCCTAGGCTACA
TCCAGCTTGGCCAGAAGGAGGGCGCAAAACTCCTCTGTGGCGGAGAGCGTTTCGGGGAGCGTGGTTTCTTCATCAAGCCT
ACTGTCTTTGGTGGCGTGCAGGATGACATGAGAATTGCCAAAGAGGAGATCTTTGGGCCTGTGCAGCCCCTGTTCAAGTT
CAAGAAGATTGAGGAGGTGATTGAGAGGGCCAACAACACCAGGTATGGCCTGGCTGCGGCTGTGTTCACCCGGGATCTGG
ACAAGGCCATGTACTTCACCCAGGCACTCCAGGCCGGGACCGTGTGGGTAAACACCTACAACATCGTCACCTGCCACACG
CCATTTGGAGGGTTTAAGGAATCTGGAAACGGGAGGGAGCTGGGTGAGGATGGGCTTAAGGCCTACACAGAGGTAAAGAC
GGTCACCATCAAGGTTCCTCAGAAGAACTCGTAA

Alignment

ORF - retro_ptro_118 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 66.87 %
• Parental protein coverage: 96.14 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  ASLHLLPSPTPNLEIKYTKIFINNEWQNSESGRVFPVYNPATGEQVCEVQEADKADIDKAVQAARLAFSL
          .S...LPSP..N..I.Y...FINNEWQ...S...FP..NP.TGE....V.E.D.AD.D.AV.AAR.AF.L
Retrocopy SSAAALPSPILNPDIPYNQLFINNEWQDAVSKKTFPTVNPTTGEVIGHVAEGDRADVDRAVKAAREAFRL

Parental  GSVWRRMDASERGRLLDKLADLVERDRAVLATMESLNGGKPFLQAFYVDLQGVIKTLRYYAGWADKIHGM
          GS.WRRMDASERGRLL..LADLVERDR..LA..E.L..GKPF......DL..VIK..RY.AGWADK.HG.
Retrocopy GSPWRRMDASERGRLLNRLADLVERDRVYLASLETLDNGKPFQESYALDLDEVIKVYRYFAGWADKWHGK

Parental  TIPVDGDYFTFTRHEPIGVCGQIIPWNFPLLMFAWKIAPALCCGNTVVIKPAEQTPLSALYMGALIKEAG
          TIP.DG..F.FTRHEP.GVCGQIIPWNFPL.M..WK.APAL..GNTVV.K.AEQTPLSALY...LIKEAG
Retrocopy TIPMDGQHFCFTRHEPVGVCGQIIPWNFPLVMQGWKLAPALATGNTVVMKVAEQTPLSALYLASLIKEAG

Parental  FPPGVINILPGYGPTAGAAIASHIGIDKIAFTGSTEVGKLIQEAAGRSNLKRVTLELGGKSPNIIFADAD
          FPPGV.NI..GYGPTAGAAIA.H...DK.AFTGSTEVG.LIQ.AAG.SNLKRVTLELGGKSP.I..ADAD
Retrocopy FPPGVVNIITGYGPTAGAAIAQHMDVDKVAFTGSTEVGHLIQKAAGDSNLKRVTLELGGKSPSIVLADAD

Parental  LDYAVEQAHQGVFFNQGQCCTAGSRIFVEESIYEEFVRRSVERAKRRIVGSPFDPTTEQGPQIDKKQYNK
          ...AVEQ.H...FFN.GQCC.AGSR.FVEESIY.EF..R.VE.AK.R.VG.PF...T.QGPQ.DK.Q...
Retrocopy MEHAVEQCHEALFFNMGQCCCAGSRTFVEESIYNEFLERTVEKAKQRKVGNPFELDTQQGPQVDKEQFER

Parental  ILELIQSGVAEGAKLECGGKGLGRKGFFIEPTVFSNVTDDMRIAKEEIFGPVQEILRFKTMDEVIERANN
          .L..IQ.G..EGAKL.CGG...G..GFFI.PTVF..V.DDMRIAKEEIFGPVQ....FK...EVIERANN
Retrocopy VLGYIQLGQKEGAKLLCGGERFGERGFFIKPTVFGGVQDDMRIAKEEIFGPVQPLFKFKKIEEVIERANN

Parental  SDFGLVAAVFTNDINKALTVSSAMQAGTVWINCYNALNAQSPFGGFKMSGNGREMGEFGLREYSEVKTVT
          ...GL.AAVFT.D..KA.....A.QAGTVW.N.YN......PFGGFK.SGNGRE.GE.GL..Y.EVKTVT
Retrocopy TRYGLAAAVFTRDLDKAMYFTQALQAGTVWVNTYNIVTCHTPFGGFKESGNGRELGEDGLKAYTEVKTVT

Parental  VKIPQKNS
          .K.PQKNS
Retrocopy IKVPQKNS

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	20.11 RPM	0.97 RPM
SRP007412_cerebellum	11.44 RPM	1.51 RPM
SRP007412_heart	12.53 RPM	13.99 RPM
SRP007412_kidney	28.69 RPM	55.91 RPM
SRP007412_liver	103.15 RPM	2.00 RPM
SRP007412_testis	3.79 RPM	271.89 RPM

ChIP-Seq

Pan troglodytes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ptro_118 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_118 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_118 has 8 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_19
Gorilla gorilla	retro_ggor_33
Pongo abelii	retro_pabe_32
Macaca mulatta	retro_mmul_247
Mus musculus	retro_mmus_222
Rattus norvegicus	retro_rnor_307
Bos taurus	retro_btau_48
Sus scrofa	retro_sscr_9

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Parental genes homology:

Parental genes homology involve 8 parental genes, and 8 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000006418	1 retrocopy	retro_chof_1106,
Erinaceus europaeus	ENSEEUG00000012262	1 retrocopy	retro_eeur_15,
Monodelphis domestica	ENSMODG00000008641	1 retrocopy	retro_mdom_254,
Pan troglodytes	ENSPTRG00000007113	1 retrocopy	retro_ptro_118 ,
Sorex araneus	ENSSARG00000012720	1 retrocopy	retro_sara_40,
Sarcophilus harrisii	ENSSHAG00000012217	1 retrocopy	retro_shar_111,
Tarsius syrichta	ENSTSYG00000004549	1 retrocopy	retro_tsyr_8,
Tursiops truncatus	ENSTTRG00000002361	1 retrocopy	retro_ttru_932,