RetrogeneDB ID: retro_ptro_2282

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: 5:91166359..91167238(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSPTRG00000039522
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: AKTIP
• Ensembl ID: ENSPTRG00000008116
• Aliases: AKTIP, FTS
• Description: AKT interacting protein [Source:HGNC Symbol;Acc:16710]

Sequence

>retro_ptro_2282
ATGAACCCTTTCTGGAGCATGTCTACAAGCTCTGTACGCAAACGATCTGAAGTTGAAGAGAAGACATTAACAGGGGACGT
GAAAACCAGTCCTCCACGAACTGCACCAAAGAAACAACTGCCTTCTATTCCCAAAAATGCTTTGCCCATAACTAAGCCTA
CATCTCCTGCCCCAGCAGCACAGTCAACAAATGGCACGCATGCGTCCTATGGACCCTTCTACCTGGAATACTCTCTTCTT
GCAGAATTTACCTTGGTTGTGAAGCAGAAGCTACCAGGCGTCTATGTGCAGCCATCTTATCGCTCTGCATTAATGTGGTT
TGGAGTAATATTCATACAGCATGGACTTTACCAAGATGGCGTATTTAAGTTTACGGTTTACATCCCTGATAACTATCCAG
ATGGTGACTGTCCACGCTTGGTGTTCGATATTCCTGTCTTTCACCCGCTAGTTGATCCCACCTCAGGTGAGCTGGACGTG
AAGAGAGCATTTGCAAAATGGAGGAGGAACCATAATCATATTTGGCAGGTATTAATGTATGCAAGGAGAGTTTTCTACAA
GATTGATAGAGCAAGCCCCCTGAACCCAGAGGCTGCAGTACTGTATGAAAAAGATATTCAGCTTTTTAAAAGTAAAGTTG
TTGACAGTGTTAAGCTGTGCACTGCTCGTTTGTTTGACCAACCTAAAATAGAAGACCTCTATGCAATTAGCTTTTCTCCA
TGGAATCCTTCTGTACATGATGAAGCTGGAGAAAAGATTCTGACTCAGAAAAAGAAGCCTGAAGAACAACACAATAAAAG
TGTTCATGTTGCTGGCCTGTCATGGGTAAAGCCTGGCTCAGTATAGCCTTTCAGTAAAGAAGCGAAAACAGTGGCGACT

Alignment

ORF - retro_ptro_2282 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 96.59 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MNPFWSMSTSSVRKRSEGEEKTLTGDVKTSPPRTAPKKQLPSIPKNALPITKPTSPAPAAQSTNGTHASY
          MNPFWSMSTSSVRKRSE.EEKTLTGDVKTSPPRTAPKKQLPSIPKNALPITKPTSPAPAAQSTNGTHASY
Retrocopy MNPFWSMSTSSVRKRSEVEEKTLTGDVKTSPPRTAPKKQLPSIPKNALPITKPTSPAPAAQSTNGTHASY

Parental  GPFYLEYSLLAEFTLVVKQKLPGVYVQPSYRSALMWFGVIFIRHGLYQDGVFKFTVYIPDNYPDGDCPRL
          GPFYLEYSLLAEFTLVVKQKLPGVYVQPSYRSALMWFGVIFI.HGLYQDGVFKFTVYIPDNYPDGDCPRL
Retrocopy GPFYLEYSLLAEFTLVVKQKLPGVYVQPSYRSALMWFGVIFIQHGLYQDGVFKFTVYIPDNYPDGDCPRL

Parental  VFDIPVFHPLVDPTSGELDVKRAFAKWRRNHNHIWQVLMYARRVFYKIDTASPLNPEAAVLYEKDIQLFK
          VFDIPVFHPLVDPTSGELDVKRAFAKWRRNHNHIWQVLMYARRVFYKID.ASPLNPEAAVLYEKDIQLFK
Retrocopy VFDIPVFHPLVDPTSGELDVKRAFAKWRRNHNHIWQVLMYARRVFYKIDRASPLNPEAAVLYEKDIQLFK

Parental  SKVVDSVKVCTARLFDQPKIEDPYAISFSPWNPSVHDEAREKMLTQ-KKPEEQHNKSVHVAGLSWVKPGS
          SKVVDSVK.CTARLFDQPKIED.YAISFSPWNPSVHDEA.EK.LTQ.KKPEEQHNKSVHVAGLSWVKPGS
Retrocopy SKVVDSVKLCTARLFDQPKIEDLYAISFSPWNPSVHDEAGEKILTQKKKPEEQHNKSVHVAGLSWVKPGS

Parental  VQPFSKEEKTVAT
          V.PFSKE.KTVAT
Retrocopy V*PFSKEAKTVAT

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	1.43 RPM	53.93 RPM
SRP007412_cerebellum	0.32 RPM	44.52 RPM
SRP007412_heart	0.29 RPM	53.60 RPM
SRP007412_kidney	0.37 RPM	32.79 RPM
SRP007412_liver	0.23 RPM	22.06 RPM
SRP007412_testis	0.53 RPM	55.96 RPM

ChIP-Seq

Pan troglodytes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ptro_2282 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_2282 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_2282 has 1 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_3152

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Parental genes homology:

Parental genes homology involve 20 parental genes, and 32 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000016345	1 retrocopy	retro_amel_392,
Canis familiaris	ENSCAFG00000009500	1 retrocopy	retro_cfam_1826,
Choloepus hoffmanni	ENSCHOG00000013690	2 retrocopies	retro_chof_2533, retro_chof_629,
Callithrix jacchus	ENSCJAG00000001498	1 retrocopy	retro_cjac_2895,
Cavia porcellus	ENSCPOG00000006523	1 retrocopy	retro_cpor_622,
Dasypus novemcinctus	ENSDNOG00000004906	4 retrocopies	retro_dnov_1376, retro_dnov_1776, retro_dnov_2080, retro_dnov_756,
Equus caballus	ENSECAG00000020381	1 retrocopy	retro_ecab_504,
Homo sapiens	ENSG00000166971	2 retrocopies	retro_hsap_1458, retro_hsap_3152,
Gorilla gorilla	ENSGGOG00000014821	1 retrocopy	retro_ggor_1122,
Microcebus murinus	ENSMICG00000010810	3 retrocopies	retro_mmur_124, retro_mmur_333, retro_mmur_985,
Microcebus murinus	ENSMICG00000016793	1 retrocopy	retro_mmur_1191,
Monodelphis domestica	ENSMODG00000025788	1 retrocopy	retro_mdom_1881,
Nomascus leucogenys	ENSNLEG00000001106	1 retrocopy	retro_nleu_2660,
Otolemur garnettii	ENSOGAG00000014495	1 retrocopy	retro_ogar_365,
Oryzias latipes	ENSORLG00000013747	1 retrocopy	retro_olat_30,
Pongo abelii	ENSPPYG00000007351	2 retrocopies	retro_pabe_1204, retro_pabe_1205,
Pan troglodytes	ENSPTRG00000008116	1 retrocopy	retro_ptro_2282 ,
Rattus norvegicus	ENSRNOG00000011956	1 retrocopy	retro_rnor_1611,
Tupaia belangeri	ENSTBEG00000017105	5 retrocopies	retro_tbel_1063, retro_tbel_2864, retro_tbel_3350, retro_tbel_4130, retro_tbel_853,
Tursiops truncatus	ENSTTRG00000012705	1 retrocopy	retro_ttru_348,