RetrogeneDB ID: retro_ptro_1457

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: 21:22155561..22156527(+)
• Located in intron of: ENSPTRG00000013884

Retrocopy information

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

Parental gene information

• Parental gene symbol: RIMKLB
• Ensembl ID: ENSPTRG00000004643
• Aliases: None
• Description: ribosomal protein S6 modification-like protein B [Source:RefSeq peptide;Acc:NP_001233444]

Sequence

>retro_ptro_1457
GAGCTAATCACTGCCTACCCACAAGTGGTGGTAGTCAGAGTACCAACCCCTTGGGTGCAAAGTGATAGTGACATCACTGT
TTTGCGCCATCTAGAGAAGATGGGATGCCAGTTAATGAACCGACCTCAAGCCATCCTGAACTGCGTTAATAAGTTCTGGA
CATTTCAAGAGTTGGCTGGCCATGGTGTTCCTCTGCCGGATACTTTCTCTTATGGTGGCCATGAAAATTTTGCTAAAATG
ATTGATAAAGCTCAAGTACTGGAGTTCCCAATGGTAGTAAAGAATACGCGGGGTCATAGAGGTAAAGCTGTTTTCTTGGC
TCGAGATAAGCACCATTTGGCTGATCTAAGCCATCTTATTTGCCATGAAGCGCCATACTTGTTCCAGAAGTATGTTAAAG
AGTCACATGGATGGGATGTACGTGTCATTGTCGTGGGAGGCCATGTGGTTGGCACCATGTTACATTGTTCAACAGATGGG
AGAATGCAAAGCAACTGCTCATTAGGTGGTGTGGGGATGATGTGTTCATTGAGTGAACAAGGGAAGCAGCTAGCTATCCA
GGTGTCTAATATCCTGGGGATGGATGTGTGTGGCATTGACCTGTTGATGAAAGATGGCGGCTCCTTCTGTGTCTGTGAGG
CCAATGCAAATGTAGGTTTCATCGCCTTTGATAAGGCTTGTAATCTAGATGTAGCTGGTATCATAGCAGACTATACTGCC
TCCCTTCTACCCTCTGGCCAGCTCACCCAGCCTATGTCCCTGCTCTCTATGGTGTCCACTGCCAGTGAGACTAGTGAGCC
GGAGCTGGGTCCCCCAGCCAGCACTGCTGTTGACAACATAAGTGCAAGTTTCAGCTCTGTTGACAGTGACCCTGAAAGCA
TGGAGCGAGAGCTGCTCACCAAACTCCCAGGGGGACTGTTCAACATGAACCAGCTGCTAGCCAATGAAATCAAACTACTG
GTGGAC

Alignment

ORF - retro_ptro_1457 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 95.03 %
• Parental protein coverage: 83.42 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  ELITAYPQVVVVRVPTPWVQSDSDITVLRHLEKMGCRLMNRPQAILNCVNKFWTFQELAGHGVPLPDTFS
          ELITAYPQVVVVRVPTPWVQSDSDITVLRHLEKMGC.LMNRPQAILNCVNKFWTFQELAGHGVPLPDTFS
Retrocopy ELITAYPQVVVVRVPTPWVQSDSDITVLRHLEKMGCQLMNRPQAILNCVNKFWTFQELAGHGVPLPDTFS

Parental  YGGHENFAKMIDEAEVLEFPMVVKNTRGHRGKAVFLARDKHHLADLSHLIRHEAPYLFQKYVKESHGRDV
          YGGHENFAKMID.A.VLEFPMVVKNTRGHRGKAVFLARDKHHLADLSHLI.HEAPYLFQKYVKESHG.DV
Retrocopy YGGHENFAKMIDKAQVLEFPMVVKNTRGHRGKAVFLARDKHHLADLSHLICHEAPYLFQKYVKESHGWDV

Parental  RVIVVGGRVVGTMLRCSTDGRMQSNCSLGGVGMMCSLSEQGKQLAIQVSNILGMDVCGIDLLMKDDGSFC
          RVIVVGG.VVGTML.CSTDGRMQSNCSLGGVGMMCSLSEQGKQLAIQVSNILGMDVCGIDLLMKD.GSFC
Retrocopy RVIVVGGHVVGTMLHCSTDGRMQSNCSLGGVGMMCSLSEQGKQLAIQVSNILGMDVCGIDLLMKDGGSFC

Parental  VCEANANVGFIAFDKACNLDVAGIIADYAASLLPSGRLTRRMSLLSVVSTASETSEPELGPPASTAVDNM
          VCEANANVGFIAFDKACNLDVAGIIADY.ASLLPSG.LT..MSLLS.VSTASETSEPELGPPASTAVDN.
Retrocopy VCEANANVGFIAFDKACNLDVAGIIADYTASLLPSGQLTQPMSLLSMVSTASETSEPELGPPASTAVDNI

Parental  SASSSSVDSDPESTERELLTKLPGGLFNMNQLLANEIKLLVD
          SAS.SSVDSDPES.ERELLTKLPGGLFNMNQLLANEIKLLVD
Retrocopy SASFSSVDSDPESMERELLTKLPGGLFNMNQLLANEIKLLVD

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	0.16 RPM	25.99 RPM
SRP007412_cerebellum	0.25 RPM	54.96 RPM
SRP007412_heart	0.00 RPM	14.28 RPM
SRP007412_kidney	0.10 RPM	23.72 RPM
SRP007412_liver	0.07 RPM	4.75 RPM
SRP007412_testis	0.32 RPM	103.59 RPM

ChIP-Seq

Pan troglodytes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ptro_1457 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_1457 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_1457 has 3 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_2506
Gorilla gorilla	retro_ggor_31
Pongo abelii	retro_pabe_1844

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Parental genes homology:

Parental genes homology involve 8 parental genes, and 9 retrocopies.

Species	Parental gene accession	Retrocopies number
Homo sapiens	ENSG00000166532	1 retrocopy	retro_hsap_2506,
Gorilla gorilla	ENSGGOG00000000332	1 retrocopy	retro_ggor_31,
Oryctolagus cuniculus	ENSOCUG00000013997	1 retrocopy	retro_ocun_1777,
Otolemur garnettii	ENSOGAG00000011440	2 retrocopies	retro_ogar_1183, retro_ogar_2985,
Pongo abelii	ENSPPYG00000004244	1 retrocopy	retro_pabe_1844,
Pan troglodytes	ENSPTRG00000004643	1 retrocopy	retro_ptro_1457 ,
Rattus norvegicus	ENSRNOG00000023814	1 retrocopy	retro_rnor_255,
Tarsius syrichta	ENSTSYG00000003996	1 retrocopy	retro_tsyr_1977,