RetrogeneDB ID: retro_pabe_2382

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: 3:173518801..173519366(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: FHL1
• Ensembl ID: ENSPPYG00000020761
• Aliases: None
• Description: four and a half LIM domains 1 [Source:HGNC Symbol;Acc:3702]

Sequence

>retro_pabe_2382
ACACATCCAAAGTGAGGTCCCTCCAGCTATAAGGTGGGCACCATGGTGGAGAAGTTTGACTGTCTCTACTGCAGGGACCC
CTTGCAGAGGAAAAAGTATGTGCAGAAGGGTGACCACCACTGCTGCCTGAAATGCTTTGACAGGTTCTGTGCCAACACCT
GCATGGAATGCTGCAAGCCCATCCGTGTGGACTCCAAGGAGGTGCACTATAAAAACTGCTTCTGGCATGACTCCTGCTTC
CACTGTGCCAAGTGCCTTCACCCCTTGCCAATGAGACCTTTGTGGCCAAGGACAACAAGATCCTGTGCAACAAGTTCGCC
ACTCAGGAGGACTCTCCCAAGTGTAAGGGGTGCTTCAAGGCCTTTGTGGCAGGAGATCAAAAATGGAGTACAACGGGACC
ATCTCGCACAAAGACTGCTTCACCTGTAGCAACTGCAAGCAAGTCATGGGGACTGGAAGCTTCTTCTCTAAAGGGAAGGA
CTTCTACTGTGTGACTTGCCATGAGACCATGTTTGCTAAACATGGTGTGAAGTGCAACAAGGCCATCGCATCTTGGGGAG
TCACC

Alignment

ORF - retro_pabe_2382 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 81.15 %
• Parental protein coverage: 55.75 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  SHRHSGPSSYKVGTMAEKFDCHYCRDPLQGKKYVQKDGHHCCLKCFDKFCANTCVECRKPIGADSKEVHY
          .H...GPSSYKVGTM.EKFDC.YCRDPLQ.KKYVQK..HHCCLKCFD.FCANTC.EC.KPI..DSKEVHY
Retrocopy THPK*GPSSYKVGTMVEKFDCLYCRDPLQRKKYVQKGDHHCCLKCFDRFCANTCMECCKPIRVDSKEVHY

Parental  KNRFWHDTCFRCAKCLH-PLANETFVAKDNKILCNKCTTREDSPKCKGCFKAIVAGDQ-NVEYKGTVWHK
          KN.FWHD.CF.CAKCLH.PLANETFVAKDNKILCNK..T.EDSPKCKGCFKA.VAGDQ...EY.GT..HK
Retrocopy KNCFWHDSCFHCAKCLH<PLANETFVAKDNKILCNKFATQEDSPKCKGCFKAFVAGDQ<KMEYNGTISHK

Parental  DCFTCSNCKQVIGTGSFFPKGEDFYCVTCHETKFAKHCVKCNKAITSGGIT
          DCFTCSNCKQV.GTGSFF.KG.DFYCVTCHET.FAKH.VKCNKAI.S.G.T
Retrocopy DCFTCSNCKQVMGTGSFFSKGKDFYCVTCHETMFAKHGVKCNKAIASWGVT

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	139.61 RPM
SRP007412_cerebellum	0.00 RPM	131.45 RPM
SRP007412_heart	0.03 RPM	726.64 RPM
SRP007412_kidney	0.00 RPM	20.48 RPM
SRP007412_liver	0.00 RPM	23.38 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_2382 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_2382 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_2382 has 3 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_2878
Gorilla gorilla	retro_ggor_1994
Macaca mulatta	retro_mmul_1458

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Parental genes homology:

Parental genes homology involve 8 parental genes, and 10 retrocopies.

Species	Parental gene accession	Retrocopies number
Dipodomys ordii	ENSDORG00000015644	2 retrocopies	retro_dord_299, retro_dord_722,
Homo sapiens	ENSG00000022267	1 retrocopy	retro_hsap_2878,
Gorilla gorilla	ENSGGOG00000010054	1 retrocopy	retro_ggor_1994,
Microcebus murinus	ENSMICG00000009342	1 retrocopy	retro_mmur_1438,
Myotis lucifugus	ENSMLUG00000014336	2 retrocopies	retro_mluc_311, retro_mluc_814,
Macaca mulatta	ENSMMUG00000007922	1 retrocopy	retro_mmul_1458,
Mus musculus	ENSMUSG00000023092	1 retrocopy	retro_mmus_51,
Pongo abelii	ENSPPYG00000020761	1 retrocopy	retro_pabe_2382 ,