RetrogeneDB ID: retro_ptro_3214

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: X:49116119..49116989(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: ACAA2
• Ensembl ID: ENSPTRG00000010016
• Aliases: None
• Description: None

Sequence

>retro_ptro_3214
TTGGCAAGGCATGTTGGTTTGCATGTGGGAATCCCAAAGGAGACCCCAGCTCTCACGATTAATAGGCTCTGTGGTTCTGG
TTTTCAGTCCACTGTGAATGGGTGTTAGGAAATTTGTGTTAAAGAAGCTGAAGTTGTTTTATGCGGAGGAACCAAAAGCA
TGAGCCAAGCTCCCTACTGTGTCAGAAATGTGTGTTTTGGAACCAAGCTTGGATCAGATATCAAGCTGGAAGATTCTTTA
TGGATAGGATTAACAGATCAGCATGTCCAGCTCCCCATGGCAATGACTGCAGAGAATCTTGCTGTAAAACATAAAATAAG
CAGAGAAGAATGTGACAAATACGGCCTGCAGTCACAGCAGAGATGGAAAGCTGCTAATGATGCTGGCTACTTTAATGATG
AAATGGCACCAATTGAAGTGAAGACAAAGAAAGGAAAACAGACAATGCAGGTAGATGAGCATGCTGGGCCCCAAACAACC
CTGGAATAGTTACAGAAACTTCCTCCAGTATTCAAGAAAGATGGTACTGTCACTGCAGGGAATGCATCGGGGATAGCTGA
TGGTGCTGGAGCTGTTATCATAGCTAGTGAAGATGCTGTTAAGAACCATAACTTCACACCACTGGCAAGAATTGTGGGCT
ACTTTGTATCTGTATGTGATCCCTCTATCATGGGTATTGGTCCTGTCCTTGCTATCAGTGGGGCACTGAAGAAAGCAGGA
CTGAGTCTTAAGGACATGGATTTGGTAGAGGTGAATGAAGCTTTTGCTCCCCAGTACTTGGCTGTTGAGAAGAGTTTGGA
TCTTGACATAAGTAAAACCAATGTGAATGGAGGAGCCATTGCTTTGGGTCACCCACTGGGAGGATCTGGA

Alignment

ORF - retro_ptro_3214 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 94.14 %
• Parental protein coverage: 73.05 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  LARHVGLRVGIPEETPALTINRLCGSGFQSIVNGCQEICVKEAEVVLCGGTESMSQAPYCVRNVRFGTKL
          LARHVGL.VGIP.ETPALTINRLCGSGFQS.VNGC.EICVKEAEVVLCGGT.SMSQAPYCVRNV.FGTKL
Retrocopy LARHVGLHVGIPKETPALTINRLCGSGFQSTVNGC*EICVKEAEVVLCGGTKSMSQAPYCVRNVCFGTKL

Parental  GSDIKLEDSLWASLTDQHVQLPMAMTAENLAVKHKISREECDKYALQSQQRWKAANDAGYFNDEMAPIEV
          GSDIKLEDSLW..LTDQHVQLPMAMTAENLAVKHKISREECDKY.LQSQQRWKAANDAGYFNDEMAPIEV
Retrocopy GSDIKLEDSLWIGLTDQHVQLPMAMTAENLAVKHKISREECDKYGLQSQQRWKAANDAGYFNDEMAPIEV

Parental  KTKKGKQTMQVDEHARPQTTLEQLQKLPPVFKKDGTVTAGNASGVADGAGAVIIASEDAVKKHNFTPLAR
          KTKKGKQTMQVDEHA.PQTTLE.LQKLPPVFKKDGTVTAGNASG.ADGAGAVIIASEDAVK.HNFTPLAR
Retrocopy KTKKGKQTMQVDEHAGPQTTLE*LQKLPPVFKKDGTVTAGNASGIADGAGAVIIASEDAVKNHNFTPLAR

Parental  IVGYFVSGCDPSIMGIGPVPAISGALKKAGLCLKDMDLVEVNEAFAPQYLAVERSLDLDISKTNVNGGAI
          IVGYFVS.CDPSIMGIGPV.AISGALKKAGL.LKDMDLVEVNEAFAPQYLAVE.SLDLDISKTNVNGGAI
Retrocopy IVGYFVSVCDPSIMGIGPVLAISGALKKAGLSLKDMDLVEVNEAFAPQYLAVEKSLDLDISKTNVNGGAI

Parental  ALGHPLGGSG
          ALGHPLGGSG
Retrocopy ALGHPLGGSG

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	0.29 RPM	19.34 RPM
SRP007412_cerebellum	0.07 RPM	8.64 RPM
SRP007412_heart	0.58 RPM	95.13 RPM
SRP007412_kidney	0.71 RPM	170.67 RPM
SRP007412_liver	2.06 RPM	176.04 RPM
SRP007412_testis	1.05 RPM	26.24 RPM

ChIP-Seq

Pan troglodytes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ptro_3214 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_3214 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_3214 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 9 parental genes, and 10 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000009411	1 retrocopy	retro_amel_602,
Equus caballus	ENSECAG00000019394	1 retrocopy	retro_ecab_454,
Homo sapiens	ENSG00000167315	1 retrocopy	retro_hsap_4829,
Gorilla gorilla	ENSGGOG00000012552	1 retrocopy	retro_ggor_3011,
Myotis lucifugus	ENSMLUG00000022960	1 retrocopy	retro_mluc_654,
Nomascus leucogenys	ENSNLEG00000011576	1 retrocopy	retro_nleu_2706,
Ochotona princeps	ENSOPRG00000007567	2 retrocopies	retro_opri_1224, retro_opri_348,
Pan troglodytes	ENSPTRG00000010016	1 retrocopy	retro_ptro_3214 ,
Vicugna pacos	ENSVPAG00000012121	1 retrocopy	retro_vpac_625,