RetrogeneDB ID: retro_ptro_383

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: 1:200779390..200780126(-)
• Located in intron of: ENSPTRG00000002005

Retrocopy information

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

Parental gene information

• Parental gene symbol: SLC35E3
• Ensembl ID: ENSPTRG00000005201
• Aliases: None
• Description: solute carrier family 35, member E3 [Source:HGNC Symbol;Acc:20864]

Sequence

>retro_ptro_383
TTATATTTGCCTCAACATGTCTGCCACCCCAAGATCCTCCTTCTGGCCTTTAGCTTCTGTGATTACAAGGTCTTCACCAA
CGTCTCTCTGCAGGGCAACTCCACAGGCGTCCATCAGCTGATCAAGGTCATCATTACACTGGTGATTATGGCCATGCAGA
CCCTCTGCCACCAGAAGGCCTTCTTCACCAGAATATAACACAACACTGATTCCTGTAACTTTAGGTGTAATCCTAAATTC
TTATTACAGTGTGAAATGTAATGTCCTTGGAAGGATGTTTTCTGCTCTCAGTGTTTTAGTTATACCCCCTTATCCAGTGT
GGGCAGAAACCAAGCAGAATGAGTTTCAAGTAAACTCAATGCTGCTGCAAGCACTATCAAGCACCAATACCTTCTGCTGT
TATTGGTTGCTTCTCTGAGTCAGTGCATGGAGAGCAAGAAATATCTGGTCTCTGGTCAGCTTCTGCTTTGCCTATGGTGC
AGCTATCTGAAATAATGGTTGTCATGGTGAACTTATCAATTTACTGGGTCACTAGGTACACTTCATCAGTCACCTATGAC
ATGTTTGGGCACTTCAAGTTCTGACTTGCTTTATTTGGAGGACATGTGTTATTTAAAGATCCACTGTTAATTAACCAGAG
TCTTGGCATTTTATGTAGTTATTTGGTGTAAGAATAAGAGCTTATATTCATTCTGTACTCTATAAACAGGAAGGAAGAAA
ATGTAAATTGCTACAA

Alignment

ORF - retro_ptro_383 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 57.37 %
• Parental protein coverage: 78.53 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  IFAPKSLPPSRLLLLALSFCGFVVFTNLSLQNNTIGTYQLAKAMTTPVIIAIQTFCYQKTFSTRI-QLTL
          ...P........LLLA.SFC...VFTN.SLQ.N..G..QL.K...T.VI.A.QT.C.QK.F.TRI...TL
Retrocopy LYLPQHVCHPKILLLAFSFCDYKVFTNVSLQGNSTGVHQLIKVIITLVIMAMQTLCHQKAFFTRI>NTTL

Parental  IPITLGVILNSYYDVKFNFLGMVFAALGVLVTSLYQVWVGAKQHELQVNSMQLL-YYQAPMSSAMLLVAV
          IP.TLGVILNSYY.VK.N.LG..F.AL.VLV...Y.VW...KQ.E.QVNSM.L...YQAP..SA...V..
Retrocopy IPVTLGVILNSYYSVKCNVLGRMFSALSVLVIPPYPVWAETKQNEFQVNSMLLQ>HYQAPIPSA---VIG

Parental  PFFEPVFGEGGIFGPWSVSALLMVLLSGVIAFMVNLSIYWIIGNTSPVTYNMF-HFKFCITLFGGYLLFK
          .F.E.V.GE..I.G.WS.SAL.MV.LS.....MVNLSIYW....TS.VTY.MF.HFKF...LFGG..LFK
Retrocopy CFSESVHGEQEISGLWSASALPMVQLSEIMVVMVNLSIYWVTRYTSSVTYDMFGHFKF*LALFGGHVLFK

Parental  DPLSINQALGILCT-LFG--ILAYTHFKLSEQEGSRSKLAQ
          DPL.INQ.LGILC..LFG..I.AY.H..L..QEG...KL.Q
Retrocopy DPLLINQSLGILCS<LFGVRIRAYIHSVLYKQEGRKCKLLQ

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	6.29 RPM
SRP007412_cerebellum	0.00 RPM	9.57 RPM
SRP007412_heart	0.00 RPM	3.99 RPM
SRP007412_kidney	0.00 RPM	9.00 RPM
SRP007412_liver	0.03 RPM	7.66 RPM
SRP007412_testis	0.21 RPM	3.48 RPM

ChIP-Seq

Pan troglodytes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ptro_383 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_383 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_383 has 3 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_513
Gorilla gorilla	retro_ggor_473
Bos taurus	retro_btau_642

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Parental genes homology:

Parental genes homology involve 8 parental genes, and 10 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000031919	1 retrocopy	retro_btau_642,
Choloepus hoffmanni	ENSCHOG00000013347	1 retrocopy	retro_chof_2348,
Cavia porcellus	ENSCPOG00000004322	3 retrocopies	retro_cpor_1404, retro_cpor_1487, retro_cpor_339,
Homo sapiens	ENSG00000175782	1 retrocopy	retro_hsap_513,
Gorilla gorilla	ENSGGOG00000012605	1 retrocopy	retro_ggor_473,
Mus musculus	ENSMUSG00000060181	1 retrocopy	retro_mmus_287,
Pan troglodytes	ENSPTRG00000005201	1 retrocopy	retro_ptro_383 ,
Pteropus vampyrus	ENSPVAG00000002545	1 retrocopy	retro_pvam_710,