RetrogeneDB ID: retro_pabe_2687

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: 5:132469186..132469982(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: LRRC59
• Ensembl ID: ENSPPYG00000008284
• Aliases: None
• Description: leucine rich repeat containing 59 [Source:HGNC Symbol;Acc:28817]

Sequence

>retro_pabe_2687
ATGACCAAGGCCAGTAGCAAGGGCGGGAACCTCCGCGACAAGCTGGACTGCAACGAACTGGACCTGAGTCTCAGTGAATG
AAGTCCCAGTGAAGGAGCTGGCTGCCCTTCCAGAGTCTACCATCCTGGATCTGTCTTGTAATAAACTGACTACTCTACTG
TCGGATTTCTGTGGCCTCACACACCTGGTGAAGCTACACCTGAGTAAGAACAAGCTGCAGGCGGACTTCAGCCGTCTAGT
CAACCTCCAGCACCTGGATCTCCTCAACAACAGGTTGGTCGCCTTGCCTGTCAGCTTTGCTCAGCTCAAGAACCTGAAGT
GGCTGGACCTGAAGGATAACTCCCTCGATCCTATCCTGGCCAAGGTGGCAAGTGACTGCTTGGATGAGAAGCAGTGTAAG
CAGTGTGCAGACACGGTGTTACAGCACAGGAAGGCTGTGCGGGAGGATCAGGAGCTGGAGAGGCAGCGGCAGTTTTAAGT
AGAACGTGAGGCAGAGAAGAAGCTTGAGGCCAAGCAGCGAGCTAAGGAACCTCAGGAGTGGGAAGCGCAGAAGCGGGAGA
AGGCGGAAGAGAAGGAGCGCCAAAGAAAGGAGTATGATGCACTCAAAGCAGCCAAGCGGGAACAAGAGAAGAAACCTAAG
AAGGAAACAAATCAGGCCCCAAAATCTAAGTCCGGCTCCCATCCCCACAAGCCACCACCCCAGAAGCACACTCATTCCTG
GGCTCTGCTGAAGCTGCTGCTGCTGCTGCTACTGTTTTGTGTGGCAGGAGGGCTGTTTGCTTGTCGGGTGACAGAG

Alignment

ORF - retro_pabe_2687 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 80.44 %
• Parental protein coverage: 87.91 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MTKAGSKGGNLRDKLDGNELDLSLS-DLNEVPVKELAALPKATILDLSCNKLTTLPSDFCGLTHLVKLDL
          MTKA.SKGGNLRDKLD.NE..L.LS...NEVPVKELAALP..TILDLSCNKLTTL.SDFCGLTHLVKL.L
Retrocopy MTKASSKGGNLRDKLDCNE--LDLS>SVNEVPVKELAALPESTILDLSCNKLTTLLSDFCGLTHLVKLHL

Parental  SKNKLQQLPADFGRLVNLQHLDLLNNRLVTLPVSFAQLKNLKWLDLKDNPLDPVLAKVAGDCLDEKQCKQ
          SKNKLQ...ADF.RLVNLQHLDLLNNRLV.LPVSFAQLKNLKWLDLKDN.LDP.LAKVA.DCLDEKQCKQ
Retrocopy SKNKLQ---ADFSRLVNLQHLDLLNNRLVALPVSFAQLKNLKWLDLKDNSLDPILAKVASDCLDEKQCKQ

Parental  CANKVLQHMKAVQADQERERQRRLEVEREAEKKREAKQRAKEAQERELRKREKAEEKERRRKEYDALKAA
          CA..VLQH.KAV..DQE.ERQR...VEREAEKK.EAKQRAKE.QE.E..KREKAEEKER.RKEYDALKAA
Retrocopy CADTVLQHRKAVREDQELERQRQF*VEREAEKKLEAKQRAKEPQEWEAQKREKAEEKERQRKEYDALKAA

Parental  KREQEKKPKK-ANQAPKSKSGSRPRKPPPRKHTRSWAVLKLLLLLLLFGVAGGLVACRVTE
          KREQEKKPKK..NQAPKSKSGS.P.KPPP.KHT.SWA..........F.VAGGL.ACRVTE
Retrocopy KREQEKKPKKETNQAPKSKSGSHPHKPPPQKHTHSWAXXXXXXXXXXFCVAGGLFACRVTE

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	0.00 RPM	22.01 RPM
SRP007412_cerebellum	0.00 RPM	11.92 RPM
SRP007412_heart	0.00 RPM	6.83 RPM
SRP007412_kidney	0.00 RPM	16.41 RPM
SRP007412_liver	0.00 RPM	19.49 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_2687 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_2687 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_2687 has 0 orthologous retrocopies within eutheria group .

---

Parental genes homology:

Parental genes homology involve 10 parental genes, and 12 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000018827	1 retrocopy	retro_cjac_2342,
Equus caballus	ENSECAG00000018072	1 retrocopy	retro_ecab_240,
Homo sapiens	ENSG00000108829	1 retrocopy	retro_hsap_3479,
Gorilla gorilla	ENSGGOG00000006310	1 retrocopy	retro_ggor_2346,
Monodelphis domestica	ENSMODG00000020901	1 retrocopy	retro_mdom_1882,
Nomascus leucogenys	ENSNLEG00000009066	1 retrocopy	retro_nleu_2629,
Pongo abelii	ENSPPYG00000008284	3 retrocopies	retro_pabe_2687 , retro_pabe_2874, retro_pabe_2875,
Pan troglodytes	ENSPTRG00000009398	1 retrocopy	retro_ptro_2985,
Tarsius syrichta	ENSTSYG00000000371	1 retrocopy	retro_tsyr_25,
Tursiops truncatus	ENSTTRG00000000207	1 retrocopy	retro_ttru_1931,