RetrogeneDB ID: retro_pabe_1693

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: 19_random:4214992..4215919(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: LSM14A
• Ensembl ID: ENSPPYG00000009832
• Aliases: LSM14A, FAM61A
• Description: Protein LSM14 homolog A [Source:UniProtKB/Swiss-Prot;Acc:Q5R4R4]

Sequence

>retro_pabe_1693
ACCTTGCCCCAGCGTATTGCGGTTGGTTCTGCTTTTACACAGGATACAAGATCTCTAAAAACACAATTATCTCAGGGTCG
TTCAAGTGCTCAGTTCGACCCTTTGAGAAGAAGCCCAACCATGGAAAAAGGAGTGCAGACCGCCTGGGCCCACTGACCTG
CTGCAGCACCTGTTGGGAGAAGGAGTCCTGTATCAACCAGGCCTTTGCCGTCTACCAGCCAAAAAGCAATAGAGAATCAG
GAGCAGAGGTGAGCTGAAGCACACAACGTTCCAAGGCCAGAAAATGAGCAATTCAGAAATGATAACAAGAGACAAGTAGC
TCCAGGTGCTCCTTCAGGGCCTAGGAGAGGGCGTGGGGGTCGTCGGGGTGGCAGGGGAGGATTTGGTATTTGGCGAGATG
GGCCAATGAAATTTGAGAAAGACTTTGACTTTGAAAGTGCAAATGCACAATTCAGCAAGGAAGAGATGGGCAGAGAGTTT
CATAATAAACTTAAATTAAAAGAAGATAAACTTGAGAAACAAGAGAAGCCTGTAAATGGTGAAGATAAAGGAGACTCAGG
AGTTGATACCCAAAACAGTGAAGGACATGCTGATGAAGAAGATCCACTTGGACCTAATTGCTATTATGACCAAACTAAAT
CCTTCTTTGATAATATTTCTTGTGATGACAATAGAGAACGGAGACCAACCTGGGCTGAAGGAAGAAGATTAAATGCTGAA
ACATTTGGAATCCCACTTTGTCCAAACCGTGGCCGTGGGGGATACAGAGGCAGAGGAGGTCTTGGTTTCCGTGGTGGCAG
AGGGCGTGGTGGTGGCAGAGGTGGTACCTTGACCACCCCTTGAGGATTTCGCGGTGGATTCAGAGGAGGTTCCAGGGGCC
GGGAGTTTGCAGATTTTGAATATAGGAAAAGCACAGCTTTGGCCCCT

Alignment

ORF - retro_pabe_1693 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 87.7 %
• Parental protein coverage: 66.74 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  TLPQSSAVGSAFTQDTRSLKTQLSQGRSSPQLDPLRKSPTMEQAVQTASAHLPAPAAVGRRSPVSTRPLP
          TLPQ..AVGSAFTQDTRSLKTQLSQGRSS.Q.DPLR.SPTME..VQTA.AH.PA.A.VGRRSPVSTRPLP
Retrocopy TLPQRIAVGSAFTQDTRSLKTQLSQGRSSAQFDPLRRSPTMEKGVQTAWAH*PAAAPVGRRSPVSTRPLP

Parental  STSQKAGENPEHRRAEVHKVSRPENEQLRNDNKRQVAPGAPSAPRRGRGGHRGGRGRFGIRRDGPMKFEK
          STSQKA.EN.E.R.AE.H.V.RPENEQ.RNDNKRQVAPGAPS.PRRGRGG.RGGRG.FGI.RDGPMKFEK
Retrocopy STSQKAIENQEQR*AEAHNVPRPENEQFRNDNKRQVAPGAPSGPRRGRGGRRGGRGGFGIWRDGPMKFEK

Parental  DFDFESANAQFNKEEIDREFHNKLKLKEDKLEKQEKPVNGEDKGDSGVDTQNSEGNADEEDPLGPNCYYD
          DFDFESANAQF.KEE..REFHNKLKLKEDKLEKQEKPVNGEDKGDSGVDTQNSEG.ADEEDPLGPNCYYD
Retrocopy DFDFESANAQFSKEEMGREFHNKLKLKEDKLEKQEKPVNGEDKGDSGVDTQNSEGHADEEDPLGPNCYYD

Parental  KTKSFFDNISCDDNRERRPTWAEERRLNAETFGIPLRPNRGRGGYRGRGGLGFRGGRGRGGGRGGTFTAP
          .TKSFFDNISCDDNRERRPTWAE.RRLNAETFGIPL.PNRGRGGYRGRGGLGFRGGRGRGGGRGGT.T.P
Retrocopy QTKSFFDNISCDDNRERRPTWAEGRRLNAETFGIPLCPNRGRGGYRGRGGLGFRGGRGRGGGRGGTLTTP

Parental  RGFRGGFRGGRGGREFADFEYRKTTAFGP
          .GFRGGFRGG..GREFADFEYRK.TA..P
Retrocopy *GFRGGFRGGSRGREFADFEYRKSTALAP

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	47.05 RPM
SRP007412_cerebellum	0.00 RPM	77.34 RPM
SRP007412_heart	0.03 RPM	36.12 RPM
SRP007412_kidney	0.03 RPM	69.71 RPM
SRP007412_liver	0.00 RPM	35.07 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_1693 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_1693 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_1693 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 12 parental genes, and 21 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000006555	1 retrocopy	retro_chof_1375,
Gorilla gorilla	ENSGGOG00000001762	1 retrocopy	retro_ggor_2378,
Microcebus murinus	ENSMICG00000011598	1 retrocopy	retro_mmur_1605,
Myotis lucifugus	ENSMLUG00000003368	1 retrocopy	retro_mluc_1793,
Macaca mulatta	ENSMMUG00000021614	2 retrocopies	retro_mmul_1386, retro_mmul_1860,
Nomascus leucogenys	ENSNLEG00000011713	4 retrocopies	retro_nleu_1299, retro_nleu_2544, retro_nleu_2580, retro_nleu_485,
Oryctolagus cuniculus	ENSOCUG00000011872	2 retrocopies	retro_ocun_193, retro_ocun_860,
Otolemur garnettii	ENSOGAG00000002492	2 retrocopies	retro_ogar_2586, retro_ogar_67,
Pongo abelii	ENSPPYG00000009832	2 retrocopies	retro_pabe_1693 , retro_pabe_2906,
Pan troglodytes	ENSPTRG00000010813	3 retrocopies	retro_ptro_1343, retro_ptro_2389, retro_ptro_863,
Rattus norvegicus	ENSRNOG00000021133	1 retrocopy	retro_rnor_2397,
Ictidomys tridecemlineatus	ENSSTOG00000002785	1 retrocopy	retro_itri_170,