RetrogeneDB ID: retro_pabe_2874

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: 6:63655385..63656054(+)
• 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_2874
ATGACTGTTCTCCCGTTGGATTTCTGTGGCCTCACACACCTGGCGAAGCTAGACCTTAGAAAGAACAAGCCACAGCACGC
ACCAGCAGACTTGGGCCATTTGGTCAACCTCCAGCACCTGGCTCTCCTCAACAACAGGCTAGTCACATTGTCTGTCAGCT
TTGCACAGCTGAAGAACCTGAAGTGGCTGGACCTGAAGGAGAACCTCTGGATCCCAGCCTGGCCAAGGTGGCAGGTGACT
GCTTGGGTGAGAAGCCATGGAAACAGCATGCAAACAAGGCATCACAGCACATGAAGGCTGTGCAGGCAGACCACCAGTAG
GAGAGGCAGCGAGGTTGGAAGTAGAACGAGAGGCAGAGAAGTATGAGGCAAAGCAGCGAGCTAAGGAAGCTCAGGAGAGG
AAATGCGGAAGCAGTAGAAGGCAGAAGAGAAGGAGTGCTGGAGAAAGCAGTATGATGCCCTCAAAGCAGCCAAGCGGGAG
CAGATGAACCCTCCCACGGAAACAAATTAGGCCCCCAAATCTAAGTCCGAATCCTGCCCCCGCAAGCCGTGCCCCCGGAA
GCACACTCATTTCTGGGCTATGCTAAAACTACTGCTGCTGCTGCTGCTGTTTTGTGCGGCGGGAGGGCTGGTTGCTTGTT
GGGTGACACAGCTACAGCAGCTGCCCCTC

Alignment

ORF - retro_pabe_2874 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 77.19 %
• Parental protein coverage: 73.53 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  LTTLPSDFCGLTHLVKLDLSKNKLQQLPADFGRLVNLQHLDLLNNRLVTLPVSFAQLKNLKWLDLKDN-P
          .T.LP.DFCGLTHL.KLDL.KNK.Q..PAD.G.LVNLQHL.LLNNRLVTL.VSFAQLKNLKWLDLK.N.P
Retrocopy MTVLPLDFCGLTHLAKLDLRKNKPQHAPADLGHLVNLQHLALLNNRLVTLSVSFAQLKNLKWLDLKEN<P

Parental  LDPVLAKVAGDCLDEKQCKQCANKVLQHMKAVQADQERERQR-RLEVEREAEKKREAKQRAKEAQER-EL
          LDP.LAKVAGDCL.EK..KQ.ANK..QHMKAVQAD...ERQR.RLEVEREAEK..EAKQRAKEAQER.E.
Retrocopy LDPSLAKVAGDCLGEKPWKQHANKASQHMKAVQADHQ*ERQR<RLEVEREAEKY-EAKQRAKEAQER<EM

Parental  RKREKAEEKERRRKEYDALKAAKREQEKKPKKANQAPKSKSGSRPRKPPPRKHTRSWAVLKLLLLLLLFG
          RK..KAEEKE..RK.YDALKAAKREQ...P...N.APKSKS.S.PRKP.PRKHT..WA.LKLLLLLLLF.
Retrocopy RKQ*KAEEKECWRKQYDALKAAKREQMNPPTETN*APKSKSESCPRKPCPRKHTHFWAMLKLLLLLLLFC

Parental  VAGGLVACRVTELQQQPL
          .AGGLVAC.VT.LQQ.PL
Retrocopy AAGGLVACWVTQLQQLPL

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	0.03 RPM	19.49 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_2874 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_2874 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_2874 has 3 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_3479
Pan troglodytes	retro_ptro_2985
Gorilla gorilla	retro_ggor_2346

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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,