RetrogeneDB ID: retro_ptro_2832

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: 9:66253507..66254430(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: GXYLT1
• Ensembl ID: ENSPTRG00000004836
• Aliases: GXYLT1, GLT8D3
• Description: None

Sequence

>retro_ptro_2832
GGTGAAAGACTGGAAGAAACTATGACCATGTTGAAGTCAGCTATTATTTTCAGGATCAAACCTCTTCAATTCCAGATTTT
TGCTGAAGATCAACTACATCATAGCTTTAAAGGAAGGCTTGACAGGGGGCATTTCTACAAATATTTAATTATACAATATA
CTCCATAACCTTTCCAAGTGAGAATGCAGCAGAGTGGAAAAACTCTTTAAACCATGTGGTTTGCAGAGATTGTCCTTGCC
GTTATTCCTGAAAGAAGTTGACTCTCACACTGATAGCCTTTTTAAAAGACCAGCTGATAATATTTGGTCTTTACTAAAGA
AATTTAATTCCACACAAATTCTGCAATGGCCCCAGAACACAAGGAATGTCAAATAGGATGGTATAGTCGCTTTGCTAGGC
ATCCATACTGTGGAAAAGCTGGAGCAAACTCTGGAGTTATGTTGACAACGTGACTTGAATGAGAAGGAAGTATTTCAAGA
ATAATATGACAACTGTGTGACTACAATGAGAAGATATGACATGGCTTAAAATATACAAGTTAAACATTACATGGGCGATC
AAGATCTGTTGGATATCCTGTTTTTTCATAATCCAGAAAGCCTTTTTGTCTTTCCGTGTCAATGGAAGTGTCGTCCAGAT
CATTGTCTATATGGAAGCAGTTGCCAAGAAGCAGAAGAAGGAATCTTTATTTTTCACGGGAACAGAGGTGTTTACCATGA
TGATAAGCAACCAGCATTTAGAGCTGTTTATGAAGCACTGAGAAATTGTTCTTTTAAGATGACAATGTTTATTCATTAAT
AAAACCTTTAGAATTGGAACTACAAAAAACAGTGCATACATACCATGGAAAAATTTACTAAATATTTATCAAACAATTAG
CAAAATCATAAGAGATCGCTATGTCAGATCACCAAAGGAAAGG

Alignment

ORF - retro_ptro_2832 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 79.94 %
• Parental protein coverage: 77.51 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 7

Retrocopy - Parental Gene Alignment:

Parental  GERLEETMTMLKSAIIFSIKPLQFHIFAEDQLHHSFKGRLDNW-SFLQTFNYTLYPITFPSENAAEWK-K
          GERLEETMTMLKSAIIF.IKPLQF.IFAEDQLHHSFKGRLD....FLQ.FNYT.Y.ITFPSENAAEWK.K
Retrocopy GERLEETMTMLKSAIIFRIKPLQFQIFAEDQLHHSFKGRLDRG<AFLQIFNYTIYSITFPSENAAEWK<K

Parental  LFKPCASQRLFLPLILKEVDSLLYVDTDILFLRPVDDIWSLLKKFNSTQI-AAMAPEHEEPRIGWYNRFA
          LFKPC..QRL.LPL.LKEVDS.....TD.LF.RP.D.IWSLLKKFNSTQI..AMAPEH.E..IGWY.RFA
Retrocopy LFKPCGLQRLSLPLFLKEVDS----HTDSLFKRPADNIWSLLKKFNSTQI<SAMAPEHKECQIGWYSRFA

Parental  RHPYYGKTGVNSGVMLM-NMTRMRRKYFKNDMTTVRLQWGDILMPLLKKYKLNITW-GDQDLLNIVFFHN
          RHPY.GK.G.NSGVML..N.T.MRRKYFKN.MTTV.LQ..D..M..LK.YKLNITW.GDQDLL.I.FFHN
Retrocopy RHPYCGKAGANSGVMLT<NVT*MRRKYFKNNMTTV*LQ*ED--MTWLKIYKLNITW<GDQDLLDILFFHN

Parental  PESLFVFPCQWNYRPDHCIYGSNCQEAEEEGIFILHGNRGVYHDDKQPAFRAVYEALRNCSFE-DDNIRS
          PESLFVFPCQW..RPDHC.YGS.CQEA.EEGIFI.HGNRGVYHDDKQPAFRAVYEALRNCSF..DDN..S
Retrocopy PESLFVFPCQWKCRPDHCLYGSSCQEA-EEGIFIFHGNRGVYHDDKQPAFRAVYEALRNCSFK<DDNVYS

Parental  LLKPLELELQKTVHTYCGKIYKIFIKQLAKS-VRDRYARSPKEK
          L.KPLELELQKTVHTY.GKIY.IFIKQLAKS..RDRY.RSPKE.
Retrocopy LIKPLELELQKTVHTYHGKIY*IFIKQLAKS<IRDRYVRSPKER

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	0.46 RPM	6.01 RPM
SRP007412_cerebellum	0.61 RPM	13.59 RPM
SRP007412_heart	0.09 RPM	7.29 RPM
SRP007412_kidney	0.21 RPM	15.25 RPM
SRP007412_liver	0.00 RPM	10.31 RPM
SRP007412_testis	0.00 RPM	18.55 RPM

ChIP-Seq

Pan troglodytes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ptro_2832 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_2832 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_2832 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 8 parental genes, and 19 retrocopies.

Species	Parental gene accession	Retrocopies number
Homo sapiens	ENSG00000151233	5 retrocopies	retro_hsap_2295, retro_hsap_4167, retro_hsap_4177, retro_hsap_4258, retro_hsap_4267,
Gorilla gorilla	ENSGGOG00000027928	3 retrocopies	retro_ggor_1702, retro_ggor_1950, retro_ggor_2798,
Monodelphis domestica	ENSMODG00000008913	1 retrocopy	retro_mdom_512,
Mus musculus	ENSMUSG00000036197	1 retrocopy	retro_mmus_2325,
Nomascus leucogenys	ENSNLEG00000017947	1 retrocopy	retro_nleu_2700,
Pongo abelii	ENSPPYG00000004419	2 retrocopies	retro_pabe_1849, retro_pabe_1976,
Pan troglodytes	ENSPTRG00000004836	5 retrocopies	retro_ptro_1623, retro_ptro_2832 , retro_ptro_2960, retro_ptro_3006, retro_ptro_848,
Rattus norvegicus	ENSRNOG00000005234	1 retrocopy	retro_rnor_2754,