RetrogeneDB ID: retro_ptro_2960

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: AACZ03187549.1:1433..2363(-)
• 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_2960
GGTGAAAGACTGGAAGAAACTATGACCGTGTTGAAGTCAGCTATTATTTTCAGGATCAAACCTCTTCAATTCCAGATTTT
TGCTGAAGATCAACTACATCATAGCTTTAAAGGAAGGCTTGACAGGGGGCATTTCTACAAATATTTAATTATACAATATA
CTCCATAACCTTTCCAAGTGAGAATGCAGCAGAGTGGAAAAGCTCTTTAAACCATGTGGTTTGCAGAGATTGTCCTTGCC
GTTATTCCTGAAAGAAGTTGACTCTCACACTGATAGCCTTTTTAAAAGACCAGCTGATAATATTTGGTTTTTACTAAAGA
AATTTAATTCCACACAAATTCTGCAATGGCCCCAGAACACAAGGAACGTCAAATAGGATGGTATAGTCGCTTTGCTAGGC
ATCCATACTGTGGAAAAGCTGGAGTAAACTCTGGAGTTATGTTGACAAACATGACTTGAATGAGAAGGAAGTATTTCAAG
AATAATATGACAACTGTGTGACTACAATGAGGAGACATACTTATGACATGGCTTAAAATGTACAAGTTAAACATTACATG
GGCGATCAAGATCTGTTGGATATCATGTTTTTTCATAATCCAGAAAGCCTTTTTGTCTTTCCGTGTCAATGGAAGTGTCA
TCCAGATCATTGTCTATGTGGAAGCAGTTGCCAAGAAGCAGAAGAAGGAATCTTTATTTTTCACGGGAACAGAGGTGTTT
ATTATGATGATAAGCAACCAGCATTTAGAGCTGTTTATGAAGCACTGAGAAATTGTTCTTTTAGGATGACAATGTTCATT
CATTAATAAAACCTTTAGAATTGGAACTACAAAAAACAGTGCATACATACCGTGGAAAAATTTACTAAATATTTATCAAA
CAATTAGCAAAAACATAAGAGATCGCTATGTCAGATCACCAAAGGAAAGG

Alignment

ORF - retro_ptro_2960 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 79.88 %
• Parental protein coverage: 77.51 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 6

Retrocopy - Parental Gene Alignment:

Parental  GERLEETMTMLKSAIIFSIKPLQFHIFAEDQLHHSFKGRLDNW-SFLQTFNYTLYPITFPSENAAEWK-K
          GERLEETMT.LKSAIIF.IKPLQF.IFAEDQLHHSFKGRLD....FLQ.FNYT.Y.ITFPSENAAEWK.K
Retrocopy GERLEETMTVLKSAIIFRIKPLQFQIFAEDQLHHSFKGRLDRG<AFLQIFNYTIYSITFPSENAAEWK<K

Parental  LFKPCASQRLFLPLILKEVDSLLYVDTDILFLRPVDDIWSLLKKFNSTQI-AAMAPEHEEPRIGWYNRFA
          LFKPC..QRL.LPL.LKEVDS.....TD.LF.RP.D.IW.LLKKFNSTQI..AMAPEH.E..IGWY.RFA
Retrocopy LFKPCGLQRLSLPLFLKEVDS----HTDSLFKRPADNIWFLLKKFNSTQI<SAMAPEHKERQIGWYSRFA

Parental  RHPYYGKTGVNSGVMLMNMTRMRRKYFKNDMTTVRLQWGDILMPLLKKYKLNITW-GDQDLLNIVFFHNP
          RHPY.GK.GVNSGVML.NMT.MRRKYFKN.MTTV.LQ.GDILM..LK.YKLNITW.GDQDLL.I.FFHNP
Retrocopy RHPYCGKAGVNSGVMLTNMT*MRRKYFKNNMTTV*LQ*GDILMTWLKMYKLNITW<GDQDLLDIMFFHNP

Parental  ESLFVFPCQWNYRPDHCIYGSNCQEAEEEGIFILHGNRGVYHDDKQPAFRAVYEALRNCSFE-DDNIRSL
          ESLFVFPCQW...PDHC..GS.CQEA.EEGIFI.HGNRGVY.DDKQPAFRAVYEALRNCSF..DDN..SL
Retrocopy ESLFVFPCQWKCHPDHCLCGSSCQEA-EEGIFIFHGNRGVYYDDKQPAFRAVYEALRNCSFR<DDNVHSL

Parental  LKPLELELQKTVHTYCGKIYKIFIKQLA-KSVRDRYARSPKEK
          .KPLELELQKTVHTY.GKIY.IFIKQLA.K..RDRY.RSPKE.
Retrocopy IKPLELELQKTVHTYRGKIY*IFIKQLA<KNIRDRYVRSPKER

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	0.02 RPM	6.01 RPM
SRP007412_cerebellum	0.00 RPM	13.59 RPM
SRP007412_heart	0.00 RPM	7.29 RPM
SRP007412_kidney	0.00 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_2960 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_2960 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_2960 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,