RetrogeneDB ID: retro_pabe_866

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: 12:80169447..80170451(+)
• Located in intron of: ENSPPYG00000004795

Retrocopy information

• Ensembl ID: ENSPPYG00000025853
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: MEST
• Ensembl ID: ENSPPYG00000018006
• Aliases: None
• Description: mesoderm specific transcript [Source:HGNC Symbol;Acc:7028]

Sequence

>retro_pabe_866
ATGGTGCGTCGAGATCGCCTCCGCAGGATGAGGGAGTGGTGGGTCCAGGTGGGGCTGCTGGCCGTGCCCCTGCTTGCTGC
GTACCTGCACATCCCAGCCCCTCAGCTCTCCCCTGCCCTTCACTCATGGAACTCTTCAGGCAAGTTTTTCACTTACAAGG
GACTGCGTATCTTCTACCAAGACTCTGTGGGAGTGGTTGGAAGTCCAGAGATAGTTGTGCTTTTACTCTGTTTTCCAACA
TCCAGCTACGATTGGTACAAGATTTGGGAAGGTCTGACCTTGAGGTTTCATCGGGTGATTGCCCTCGACTTCTTAGGCTT
TGGCTTCAGTGACAAACCGAGACCACATCACTATTCCATATTTGAGCAGGCCAGCATCGTGGAAGCGCTTTTGCGGCATC
TGGGGCTCCAGAATCGCAGGATCAACCTTCTTTCTCATGACTATGGAGATATTGTTGCGCAGGAGCTTCTCTACAGGTAC
AAGCAGAATCGATCTGGTCGGCTTACCATAAAGAGTCTCTGTCTGTCAAATGGAGGTATCTTTCCTGAGACTCACCGTCC
ACTCCTTCTCCAAAAGCTACTCAAAGATGGAGGTGTGCTGTCACCTATCCTCACACGACTAATGAACTTCTTTGTATTCT
CTCGAGGTCTCACCCCAGTCTTTGGGCCGTATACTCGGCCCTCTGAGAGTGAGCTGTGGGACATGTGGGCAGGGATCCGC
AACAATAACGGGAACTTAGTCACTGACAGTCTCTTACAGTACATCAATCAGAGGAAAAGTTCAGAAGGCGCTGGGTGGGA
GCTCTTGCCTCTGTAACTATCCCCATTCATTTTATCTATGGGCCATTGGATCCTGTAAATCCCTATCCAGAGTTTTTGGA
GCTGTACAGGAAAACGCTGCCGCGGTCCACAGTGTCAATTCTGGATGACCACATTAGCCACTATCCACAGCTAGAGGATC
CCATGGGCTTCTTGAATGCATATATGGGCTTCATCAACTCCTTC

Alignment

ORF - retro_pabe_866 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 97.92 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MVRRDRLRRMREWWVQVGLLAVPLLAAYLHIPPPQLSPALHSWKSSGKFFTYKGLRIFYQDSVGVVGSPE
          MVRRDRLRRMREWWVQVGLLAVPLLAAYLHIP.PQLSPALHSW.SSGKFFTYKGLRIFYQDSVGVVGSPE
Retrocopy MVRRDRLRRMREWWVQVGLLAVPLLAAYLHIPAPQLSPALHSWNSSGKFFTYKGLRIFYQDSVGVVGSPE

Parental  IVVLLHGFPTSSYDWYKIWEGLTLRFHRVIALDFLGFGFSDKPRPHHYSIFEQASIVEALLRHLGLQNRR
          IVVLL..FPTSSYDWYKIWEGLTLRFHRVIALDFLGFGFSDKPRPHHYSIFEQASIVEALLRHLGLQNRR
Retrocopy IVVLLLCFPTSSYDWYKIWEGLTLRFHRVIALDFLGFGFSDKPRPHHYSIFEQASIVEALLRHLGLQNRR

Parental  INLLSHDYGDIVAQELLYRYKQNRSGRLTIKSLCLSNGGIFPETHRPLLLQKLLKDGGVLSPILTRLMNF
          INLLSHDYGDIVAQELLYRYKQNRSGRLTIKSLCLSNGGIFPETHRPLLLQKLLKDGGVLSPILTRLMNF
Retrocopy INLLSHDYGDIVAQELLYRYKQNRSGRLTIKSLCLSNGGIFPETHRPLLLQKLLKDGGVLSPILTRLMNF

Parental  FVFSRGLTPVFGPYTRPSESELWDMWAGIRNNDGNLVIDSLLQYINQRK-KFRRRWVGALASVTIPIHFI
          FVFSRGLTPVFGPYTRPSESELWDMWAGIRNN.GNLV.DSLLQYINQRK.KFRRRWVGALASVTIPIHFI
Retrocopy FVFSRGLTPVFGPYTRPSESELWDMWAGIRNNNGNLVTDSLLQYINQRK<KFRRRWVGALASVTIPIHFI

Parental  YGPLDPVNPYPEFLELYRKTLPRSTVSILDDHISHYPQLEDPMGFLNAYMGFINSF
          YGPLDPVNPYPEFLELYRKTLPRSTVSILDDHISHYPQLEDPMGFLNAYMGFINSF
Retrocopy YGPLDPVNPYPEFLELYRKTLPRSTVSILDDHISHYPQLEDPMGFLNAYMGFINSF

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	0.11 RPM	19.02 RPM
SRP007412_cerebellum	0.00 RPM	18.36 RPM
SRP007412_heart	0.00 RPM	0.84 RPM
SRP007412_kidney	0.10 RPM	8.52 RPM
SRP007412_liver	0.03 RPM	10.01 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_866 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_866 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_866 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 14 parental genes, and 33 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000005659	2 retrocopies	retro_amel_1177, retro_amel_1874,
Callithrix jacchus	ENSCJAG00000010760	2 retrocopies	retro_cjac_1563, retro_cjac_3931,
Felis catus	ENSFCAG00000022984	5 retrocopies	retro_fcat_1067, retro_fcat_1645, retro_fcat_1693, retro_fcat_2004, retro_fcat_326,
Loxodonta africana	ENSLAFG00000006066	3 retrocopies	retro_lafr_578, retro_lafr_584, retro_lafr_748,
Macropus eugenii	ENSMEUG00000008227	1 retrocopy	retro_meug_885,
Microcebus murinus	ENSMICG00000006129	1 retrocopy	retro_mmur_1091,
Macaca mulatta	ENSMMUG00000009499	2 retrocopies	retro_mmul_1936, retro_mmul_94,
Nomascus leucogenys	ENSNLEG00000012841	3 retrocopies	retro_nleu_1065, retro_nleu_515, retro_nleu_790,
Otolemur garnettii	ENSOGAG00000009224	1 retrocopy	retro_ogar_3464,
Pongo abelii	ENSPPYG00000018006	4 retrocopies	retro_pabe_2337, retro_pabe_2510, retro_pabe_2511, retro_pabe_866 ,
Pan troglodytes	ENSPTRG00000019698	2 retrocopies	retro_ptro_1769, retro_ptro_2045,
Sorex araneus	ENSSARG00000000502	1 retrocopy	retro_sara_352,
Ictidomys tridecemlineatus	ENSSTOG00000020977	2 retrocopies	retro_itri_1210, retro_itri_1610,
Tursiops truncatus	ENSTTRG00000004934	4 retrocopies	retro_ttru_1026, retro_ttru_1115, retro_ttru_1133, retro_ttru_1907,