RetrogeneDB ID: retro_ptro_3173

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: X:146399351..146400434(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: TRMT1
• Ensembl ID: ENSPTRG00000010557
• Aliases: None
• Description: None

Sequence

>retro_ptro_3173
GCTATGATCATCCAGTTTGCTCGCATTCAGCTTGGGGCCAAAGGAATCCAGATCAAGGTGCCAGGAGAGAAGGATACACA
AAAGGTGGTCGTGGAATTGTCAAAGCAAGAGGAGGAAAAGGTTGAACCGAAAGGGAGTGAAAACCTGGCCTCAGGAGACC
AGCCTCGCACAGCGACCGTGTGGGAGATCTGTGAGGAAGGCCTGCATGTGCTGGAAGGCCTGGCAGCTTCAGGCCTACTT
TCCATTCGATTTGCCCTAGAGGTGCCTGGGGCTCAGATCTGTGGTTGCAAACGATACCTCTGCCGGGGCTGTGGATCTCA
TACGCTGGAATGTGCAGCTCAATGACGGGCCCACCTGGTACAGCCCAGCCAAGTAGATGGCTGGATGCTGATGTACCAGC
ACCAGAGGGTGTCAGAGAGGTTCGACGTCACCCATCTGGACCCCTATGGCAGTCCTGCCCCCTTCCTGGATGCAGCTGTG
CTGGCTGTGAGTGAAGGAGAGTTGCTGTGCGTGACCCGCACGGACACGGCGGTGCTGGCGCGGAACAGTGGGGAGATGTG
TTACAGCAAATTCGGTGCCATGGCCCTCAAGAGCCGGGCCTGCCACGAGATGGCCCTGAGAATTGTCCTGCACAGCCTGG
ACCTCCGCGCCAACTGTTACCAGCGCTTCGTGGTACCGCTGCTTAGCATCAGCGCCGACTTCTACGTGCGTGTTTTTGTC
CGTGTCTTCACCGGCCAGCCCAAGGTTAAGGCCTCAGCCAGCAAGCAGGCCCTGGTGTTCCATTGAGTGGGCTGCGGGTC
CTTCCACCTTCAGCGCCTCGGCAAAGCGTCAGGAGTCCCCCGCGGCCGGGTCAAGTCCTCTGTAGCCTGTGTTCCCCCCG
TGACCCCGAGCGTGAACACTGTGGGCAGCGACACCAGCTTGGTTGCTCCATGTGGGCAGAGCCCATCCATGACCTGGATT
TCGTGGGCTGCGTCCTAGAGGCTGTGAGCGCTAACCCCGGCCGCTTCCACACCTCGGAGCGGATGCCAGAGGGTCCTGAG
CGTCATGACTGAGGAGCTCCCAGAAGTGCCTCTCTGTACTACA

Alignment

ORF - retro_ptro_3173 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 86.03 %
• Parental protein coverage: 54.78 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  AVITEFARIQLGAKGIQIKVPGEKDTQKVVVDLSEQEEEKVELKESENLASGDQPRTAAVGEICEEGLHV
          A.I..FARIQLGAKGIQIKVPGEKDTQKVVV.LS.QEEEKVE.K.SENLASGDQPRTA.V.EICEEGLHV
Retrocopy AMIIQFARIQLGAKGIQIKVPGEKDTQKVVVELSKQEEEKVEPKGSENLASGDQPRTATVWEICEEGLHV

Parental  LEGLAASGLRSIRFALEVP-GLRSVVANDASTRAVDLIRRNVQLND-VAHLVQPSQADARMLMYQHQRVS
          LEGLAASGL.SIRFALEVP.GLRSVVAND.S..AVDLIR.NVQLND..AHLVQPSQ.D..MLMYQHQRVS
Retrocopy LEGLAASGLLSIRFALEVP>GLRSVVANDTSAGAVDLIRWNVQLND<RAHLVQPSQVDGWMLMYQHQRVS

Parental  ERFDVIDLDPYGSPATFLDAAVQAVSEGGLLCVTCTDMAVLAGNSGETCYSKYGAMALKSRACHEMALRI
          ERFDV..LDPYGSPA.FLDAAV.AVSEG.LLCVT.TD.AVLA.NSGE.CYSK.GAMALKSRACHEMALRI
Retrocopy ERFDVTHLDPYGSPAPFLDAAVLAVSEGELLCVTRTDTAVLARNSGEMCYSKFGAMALKSRACHEMALRI

Parental  VLHSLDLRANCYQRFVVPLLSISADFYVRVFVRVFTGQAKVKASASKQALVFQCVGCGAFHLQRLGKASG
          VLHSLDLRANCYQRFVVPLLSISADFYVRVFVRVFTGQ.KVKASASKQALVF..VGCG.FHLQRLGKASG
Retrocopy VLHSLDLRANCYQRFVVPLLSISADFYVRVFVRVFTGQPKVKASASKQALVFH*VGCGSFHLQRLGKASG

Parental  VPSGRVKFSAACGPPVT-PECEHCGQRHQLGGPMWAEPIHDLDFVGRVLEAVSANPGRFHTSERI-RGVL
          VP.GRVK.S.AC.PPVT.PE.EHCGQRHQLG..MWAEPIHDLDFVG.VLEAVSANPGRFHTSER....VL
Retrocopy VPRGRVKSSVACVPPVT<PEREHCGQRHQLGCSMWAEPIHDLDFVGCVLEAVSANPGRFHTSERM>QRVL

Parental  SVITEELPDVPLYYT
          SV.TEELP.VPL..T
Retrocopy SVMTEELPEVPLCTT

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	43.33 RPM
SRP007412_cerebellum	0.00 RPM	26.13 RPM
SRP007412_heart	0.00 RPM	7.14 RPM
SRP007412_kidney	0.00 RPM	23.80 RPM
SRP007412_liver	0.00 RPM	27.07 RPM
SRP007412_testis	0.00 RPM	22.66 RPM

ChIP-Seq

Pan troglodytes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ptro_3173 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_3173 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_3173 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 4 parental genes, and 4 retrocopies.

Species	Parental gene accession	Retrocopies number
Homo sapiens	ENSG00000104907	1 retrocopy	retro_hsap_4766,
Oryctolagus cuniculus	ENSOCUG00000021934	1 retrocopy	retro_ocun_1629,
Pongo abelii	ENSPPYG00000009622	1 retrocopy	retro_pabe_3709,
Pan troglodytes	ENSPTRG00000010557	1 retrocopy	retro_ptro_3173 ,