RetrogeneDB ID: retro_pabe_2150

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: 2b:99810351..99810849(-)
• Located in intron of: ENSPPYG00000013126

Retrocopy information

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

Parental gene information

• Parental gene symbol: MYL6B
• Ensembl ID: ENSPPYG00000004646
• Aliases: None
• Description: myosin, light chain 6B, alkali, smooth muscle and non-muscle [Source:HGNC Symbol;Acc:29823]

Sequence

>retro_pabe_2150
ATCCCCCAGGCCCCTGAGAAAACCAAGGAGCCCCCAGTTGATCTCTCAAAAGTGGTGATCAAGTTTAACAAGGACCAGCT
GGAGGAGTTCAAAGTGGCCTTCAAGCTGTTTAACTGAGTGGGGGATGGCAAGATCCTATACAGCCAGTTTGGGGACATGA
TGGGGGCCCTGGACCAGAACCTCACCAGTGCCAAGGTGATGAAGGTCCTGGGGAACCCCAAGAGTGATGAGCTGAAGTCC
CGGCATGTGGACTTCAAGACTTTCCTGCCCATGCTCCAGGCAGCAGCCAAGAAGCGGAACCAAGGCACATATGAGGACTA
CTCGGAGGGGCTTCATGTGTTAGTCAAGGAGGGGAACAGCAAAGTCACGGGAGCAGAGCTCAGACAAGTCCTCACCACCC
TGGAAGAGAAGATGGCTGAGGAGGAGATGGAGACTGTTCTGGCAGGACATGAGGACAGCATCAACTAGGAGGCCTTCCTG
AAACACTTCCTAAGCTTA

Alignment

ORF - retro_pabe_2150 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 78.11 %
• Parental protein coverage: 81.25 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  VPQAPQKTQEPPVDLSKVVIEFNKDQLEEFKEAFELFDRVGDGKILYSQCGDVMRALGQNPTNAEVLKVL
          .PQAP.KT.EPPVDLSKVVI.FNKDQLEEFK.AF.LF..VGDGKILYSQ.GD.M.AL.QN.T.A.V.KVL
Retrocopy IPQAPEKTKEPPVDLSKVVIKFNKDQLEEFKVAFKLFN*VGDGKILYSQFGDMMGALDQNLTSAKVMKVL

Parental  GNPKSDELKSRRVDFETFLPMLQAVAKNRGQGTYEDYLEGLRVFDKEGNGKVMGAELRHVLTTLGEKMTE
          GNPKSDELKSR.VDF.TFLPMLQA.AK.R.QGTYEDY.EGL.V..KEGN.KV.GAELR.VLTTL.EKM.E
Retrocopy GNPKSDELKSRHVDFKTFLPMLQAAAKKRNQGTYEDYSEGLHVLVKEGNSKVTGAELRQVLTTLEEKMAE

Parental  EEVETVLAGHEDSNGCINYEAFLKHILSV
          EE.ETVLAGHEDS...IN.EAFLKH.LS.
Retrocopy EEMETVLAGHEDS---IN*EAFLKHFLSL

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	74.53 RPM
SRP007412_cerebellum	0.00 RPM	25.66 RPM
SRP007412_heart	0.06 RPM	10.27 RPM
SRP007412_kidney	0.00 RPM	15.38 RPM
SRP007412_liver	0.03 RPM	3.21 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_2150 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_2150 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_2150 has 5 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_2383
Pan troglodytes	retro_ptro_1741
Gorilla gorilla	retro_ggor_1808
Macaca mulatta	retro_mmul_962
Callithrix jacchus	retro_cjac_2848

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Parental genes homology:

Parental genes homology involve 15 parental genes, and 25 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000000110	1 retrocopy	retro_cfam_1894,
Callithrix jacchus	ENSCJAG00000011620	3 retrocopies	retro_cjac_113, retro_cjac_2566, retro_cjac_2848,
Dasypus novemcinctus	ENSDNOG00000007592	1 retrocopy	retro_dnov_2073,
Homo sapiens	ENSG00000196465	1 retrocopy	retro_hsap_2383,
Gorilla gorilla	ENSGGOG00000003277	2 retrocopies	retro_ggor_1808, retro_ggor_2233,
Loxodonta africana	ENSLAFG00000012658	1 retrocopy	retro_lafr_734,
Macaca mulatta	ENSMMUG00000005214	1 retrocopy	retro_mmul_962,
Nomascus leucogenys	ENSNLEG00000026948	1 retrocopy	retro_nleu_369,
Oryctolagus cuniculus	ENSOCUG00000017368	1 retrocopy	retro_ocun_374,
Otolemur garnettii	ENSOGAG00000001521	3 retrocopies	retro_ogar_1918, retro_ogar_3179, retro_ogar_680,
Procavia capensis	ENSPCAG00000005927	2 retrocopies	retro_pcap_223, retro_pcap_242,
Pongo abelii	ENSPPYG00000004646	1 retrocopy	retro_pabe_2150 ,
Pongo abelii	ENSPPYG00000004647	3 retrocopies	retro_pabe_1467, retro_pabe_1864, retro_pabe_538,
Pan troglodytes	ENSPTRG00000023043	2 retrocopies	retro_ptro_1741, retro_ptro_2579,
Rattus norvegicus	ENSRNOG00000028837	2 retrocopies	retro_rnor_1432, retro_rnor_216,