RetrogeneDB ID: retro_pabe_130

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: 6:79795242..79795965(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSPPYG00000025883
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSPPYG00000017191
• Aliases: None
• Description: Proteasome subunit beta type [Source:UniProtKB/TrEMBL;Acc:H2PXL7]

Sequence

>retro_pabe_130
ATGTTGTCCTCTACAGCCATGTATTCGGCTCCTGGCAGAGACTTGGGGATGGAACCGCACAGAGCCGCGGGCCCTTTGCA
GCTGCGATTTTCGCCCTACGTTTTCAACGGAGGTACTGTACTGGCAATTGCTGGAGAAGATTTTGCAATTGTTGCTTCTG
ATACTCGATTGAGTGAAGGGTTTTCAATTCATACGCGGGATAGCCCCAAATGTTACAAATTAACAGACAAAACAGTCATT
GGATGCAGCGGTTTTCATGGAGACTGTCTTACGCTGACAAAGATTATTGAAGCAAGACTAAAGATGTATAAGCATTCCAA
TAATAAGGCCATGACTACGGGGGCAATTGCTGCAATGCTGTCTACAATCCTGTATTCAAGGCGCTTCTTTCCATACTATG
TTTACAACATCATCGGTGGACTTGATGAAGAAGGAAAGGGGGCTGTATACAGCTTTGACCCAGTAGGGTCTTACCAGAGA
GACTCCTTCAAGGCTGGAGGCTCAGCAAGTGCCATGCTACAGCCCCTGCTTGACAACCAGGTTGGTTTTAAGAACATGCA
GAATGTGGAGCATGTTCCGCTGTCCTTGGACAGAGCCATGCGGCTGGTGAAAGATGTCTTCATTTCTGCAGCTGAGAGAG
ATGTGTACACTGGGGACGCACTCCGGATCTGCATAGTGACCAAAGAGGGCATCAGGGAGGAGACTGTTCCCTTAAGGAAG
GAC

Alignment

ORF - retro_pabe_130 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

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

Retrocopy - Parental Gene Alignment:

Parental  MLSSTAMYSAPGRDLGMEPHRAAGPLQLRFSPYVFNGGTVLAIAGEDFAIVASDTRLSEGFSIHTRDSPK
          MLSSTAMYSAPGRDLGMEPHRAAGPLQLRFSPYVFNGGTVLAIAGEDFAIVASDTRLSEGFSIHTRDSPK
Retrocopy MLSSTAMYSAPGRDLGMEPHRAAGPLQLRFSPYVFNGGTVLAIAGEDFAIVASDTRLSEGFSIHTRDSPK

Parental  CYKLTDKTVIGCSGFHGDCLTLTKIIEARLKMYKHSNNKAMTTGAIAAMLSTILYSRRFFPYYVYNIIGG
          CYKLTDKTVIGCSGFHGDCLTLTKIIEARLKMYKHSNNKAMTTGAIAAMLSTILYSRRFFPYYVYNIIGG
Retrocopy CYKLTDKTVIGCSGFHGDCLTLTKIIEARLKMYKHSNNKAMTTGAIAAMLSTILYSRRFFPYYVYNIIGG

Parental  LDEEGKGAVYSFDPVGSYQRDSFKAGGSASAMLQPLLDNQVGFKNMQNVEHVPLSLDRAMRLVKDVFISA
          LDEEGKGAVYSFDPVGSYQRDSFKAGGSASAMLQPLLDNQVGFKNMQNVEHVPLSLDRAMRLVKDVFISA
Retrocopy LDEEGKGAVYSFDPVGSYQRDSFKAGGSASAMLQPLLDNQVGFKNMQNVEHVPLSLDRAMRLVKDVFISA

Parental  AERDVYTGDALRICIVTKEGIREETVPLRKD
          AERDVYTGDALRICIVTKEGIREETVPLRKD
Retrocopy AERDVYTGDALRICIVTKEGIREETVPLRKD

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	0.06 RPM	5.81 RPM
SRP007412_cerebellum	0.12 RPM	7.05 RPM
SRP007412_heart	0.09 RPM	4.97 RPM
SRP007412_kidney	0.00 RPM	8.02 RPM
SRP007412_liver	0.09 RPM	14.87 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_130 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_130 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_130 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 14 parental genes, and 16 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000017047	1 retrocopy	retro_amel_1066,
Canis familiaris	ENSCAFG00000004116	1 retrocopy	retro_cfam_2108,
Callithrix jacchus	ENSCJAG00000020644	1 retrocopy	retro_cjac_632,
Dasypus novemcinctus	ENSDNOG00000019502	1 retrocopy	retro_dnov_2087,
Felis catus	ENSFCAG00000031269	1 retrocopy	retro_fcat_911,
Gorilla gorilla	ENSGGOG00000022128	1 retrocopy	retro_ggor_1661,
Microcebus murinus	ENSMICG00000007469	1 retrocopy	retro_mmur_173,
Macaca mulatta	ENSMMUG00000019919	1 retrocopy	retro_mmul_1135,
Mustela putorius furo	ENSMPUG00000007150	1 retrocopy	retro_mputfur_1196,
Mus musculus	ENSMUSG00000014769	2 retrocopies	retro_mmus_1784, retro_mmus_3664,
Oryctolagus cuniculus	ENSOCUG00000007973	2 retrocopies	retro_ocun_1029, retro_ocun_620,
Procavia capensis	ENSPCAG00000000344	1 retrocopy	retro_pcap_329,
Pongo abelii	ENSPPYG00000017191	1 retrocopy	retro_pabe_130 ,
Vicugna pacos	ENSVPAG00000006517	1 retrocopy	retro_vpac_521,