RetrogeneDB ID: retro_ptro_2892

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: 9:38138365..38138969(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSPTRG00000040824
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: RAB1B
• Ensembl ID: ENSPTRG00000003915
• Aliases: None
• Description: None

Sequence

>retro_ptro_2892
ATGAACCCCGGATAGGACTGCCTGTTTAAGCTGCTTTTGATTGGCGACTCAGGCGTGGGCAAGTCATGCCTGCTCCTGCG
GTTTGCTGATGACCCGTACACAGAGAGCTACATCAGCACCATCGGGGTGGACTTCAAGATCCAAACCATCGAGCTGGATG
GCAAAACTATCAAACTTCAGATGTGGGACACGGCGGGCCAGGAACGGTTCTGGACCACCACTTCCAGCTACTACCGGGGG
GGCTCATGGCTTCCTCGTGGTATATGACGTCACTGACCAGGAATCCTACGCCAACATGAAGCAGTGGCTGCAGGAGATTG
ACTGCTATGCCAGCAAGAACGTCAATAAGCTCCTGGTGGGCAACAAGAGCGACCTCACCACCAAGAAGGTGGTGGACAAC
ACCACAGCCAAGGAGTTTGCAGACTCTTTGGGCATCCCCTTCTTGGAGACGAGTGCCAAGAATGCCACCAATGTCGAGCA
GGCGTTCATGACCATGGCTGCTGAGATCAAAAAGCAGATGGGGCCCGGAGCAGCCTCCGGGGGCGAGCGGCCCAATCTCA
AGATCGACAGCACCCCTGTAAAGCCGGCTGGCTGTGGTTGTTGC

Alignment

ORF - retro_ptro_2892 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 92.08 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MNPEYDYLFKLLLIGDSGVGKSCLLLRFADDTYTESYISTIGVDFKIRTIELDGKTIKLQIWDTAGQERF
          MNP..D.LFKLLLIGDSGVGKSCLLLRFADD.YTESYISTIGVDFKI.TIELDGKTIKLQ.WDTAGQERF
Retrocopy MNPG*DCLFKLLLIGDSGVGKSCLLLRFADDPYTESYISTIGVDFKIQTIELDGKTIKLQMWDTAGQERF

Parental  RTITSSYYRG-AHGIIVVYDVTDQESYANVKQWLQEIDRYASENVNKLLVGNKSDLTTKKVVDNTTAKEF
          .T.TSSYYRG.AHG..VVYDVTDQESYAN.KQWLQEID.YAS.NVNKLLVGNKSDLTTKKVVDNTTAKEF
Retrocopy WTTTSSYYRG>AHGFLVVYDVTDQESYANMKQWLQEIDCYASKNVNKLLVGNKSDLTTKKVVDNTTAKEF

Parental  ADSLGIPFLETSAKNATNVEQAFMTMAAEIKKRMGPGAASGGERPNLKIDSTPVKPAGGGCC
          ADSLGIPFLETSAKNATNVEQAFMTMAAEIKK.MGPGAASGGERPNLKIDSTPVKPAG.GCC
Retrocopy ADSLGIPFLETSAKNATNVEQAFMTMAAEIKKQMGPGAASGGERPNLKIDSTPVKPAGCGCC

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	0.07 RPM	136.24 RPM
SRP007412_cerebellum	0.04 RPM	104.10 RPM
SRP007412_heart	0.00 RPM	59.20 RPM
SRP007412_kidney	0.05 RPM	144.04 RPM
SRP007412_liver	0.00 RPM	113.39 RPM
SRP007412_testis	0.11 RPM	70.40 RPM

ChIP-Seq

Pan troglodytes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ptro_2892 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_2892 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_2892 has 3 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_4252
Gorilla gorilla	retro_ggor_2850
Pongo abelii	retro_pabe_3386

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Parental genes homology:

Parental genes homology involve 12 parental genes, and 13 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000001599	1 retrocopy	retro_cjac_931,
Homo sapiens	ENSG00000174903	1 retrocopy	retro_hsap_4252,
Gorilla gorilla	ENSGGOG00000009755	2 retrocopies	retro_ggor_1792, retro_ggor_2850,
Macropus eugenii	ENSMEUG00000000023	1 retrocopy	retro_meug_1985,
Monodelphis domestica	ENSMODG00000008371	1 retrocopy	retro_mdom_196,
Pongo abelii	ENSPPYG00000003031	1 retrocopy	retro_pabe_3386,
Pan troglodytes	ENSPTRG00000001370	1 retrocopy	retro_ptro_681,
Pan troglodytes	ENSPTRG00000003915	1 retrocopy	retro_ptro_2892 ,
Pan troglodytes	ENSPTRG00000011989	1 retrocopy	retro_ptro_1727,
Sarcophilus harrisii	ENSSHAG00000010376	1 retrocopy	retro_shar_68,
Ictidomys tridecemlineatus	ENSSTOG00000011052	1 retrocopy	retro_itri_1677,
Drosophila melanogaster	FBgn0016700	1 retrocopy	retro_dmel_36,