RetrogeneDB ID: retro_pabe_2280

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: 3:2067566..2069442(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: RHBDF1
• Ensembl ID: ENSPPYG00000006895
• Aliases: None
• Description: rhomboid 5 homolog 1 (Drosophila) [Source:HGNC Symbol;Acc:20561]

Sequence

>retro_pabe_2280
GATGGCACCTTGCGCCAGGCACAGCGTCGAAGCTTCACTCCAGCCAGCTCTCTGGCAGAGGACACGAATTTCCCTGATGA
GCTGGACACATCCTTCTTTGCCCAGGAAGGTATCCTCCATGAAGAGCTGTCCATATACCCGGACGAAGTTTTTGAGTCCC
CATCAGAGGCAGCACTCAAGGACTGGGAGAAGGCGCGGGAGCAGGAGTACCTCACTGGAGGGGCCCTGGACCGCAGTGAG
CTTGAGCGCAGCCACCCGATGCTGCCTTTGGAGCGAGGCTGGCGGAAGCAGAAGGAAGACACCGTAGCCTCGCAGCCCAA
GGTGCGGCTGCGACAGGAGATGGTGAGCACCGCGGGGCCGCCGCGGAACCAGCGCATCGCGATGCCTGTGCGCAAGCTCT
TCGCCCGGGAGAAGTGGTTGTATGGGCTGAGCAAGGTAGGACCGCTCACCATCCACACCTACCACAAGCACATCGACAGC
TTCGTCAAGCGACAGATTGAGGACATGGACAGCCACAGGCCCTTCTTCACCTACTGGCTCACCTTCGTGCACTCGCTCGT
CACCATTCTAGCCTTGTGCATCTATGGCATCATGCCCGTGGGCTTCTCACAGCATGAAACGGTGGACTCGGTGCTGTGGA
ACCACTGGGTCTACGAGAACGTCAAGTACGTGCAGCAGGAGAACTTCTGGATCGGGCCCAGCTCGGAGGCCCTCATCCAC
CTGGACGACAAGTTTTCGCCCTGCATATGCCAGGATCCGCAGGTGCACAGCTTCATTTGCGCAGGGCGCGAGCGGGAGAA
GCACTCGGCCTGCTGCATGCACAACAACAGGTTGGGCTGCCTGCAGACCTCGGAGGAGGAGTGCTCGTTCATGCTGGCAA
TGTGGGTGAAGTGGCCCATCCATTCCAGCGCCCCAGAGCTTGCCAGCCACAAGAGTCAGTTTGGCTCTGTCTGCCACTAG
GATCCCAGGGTATGTGATGAGCCCTCCTGGGAAGACCCCCATGAGTGGCCAGAAGACATCACCAAGTGGCCGATCTGCAC
CAAAAAAACAGTCTGGGAACCATACCAACCTTCCCCACAAGGACTGTGACATCACAGGACGGCCCTGCTGCATTGGCACC
AAGGGCAAGTGTGAGATCACCTCCCGGGAGCACTGTGACTTCATGAGGGGCTATTTCCATGAGGAGGCCACGCTCTGCTC
TCAGGTGCACTGCATGGATGATGTATGTGGGCTCCCGCCTTTCCTCAACCCTGAGGTGCCTGACCAGTTCTACTGCCTGT
GGCTGTCCCTCTTCCTGCACACTAGGATCCTGCACTGCCTGGTGTCCATCTGCTTCCAGATGACCGTCCTGCGGGTCCTG
GAGAAGCTGGCAGGGTGGCACCGCATAGCCATCATCTACCTGCTGAGTGGTGTCACTGGCAACCGGGCCAGTGTCATCTT
CCTGCTGTACCGAGCAGAGGTGGTTCCGTCTGGCTCTTAGTTTGGCATCCTGGCCTGCCTCTTCGTGGAGCTCTTCCAGA
GCTGGCAGATCCTGGAGCGGCCCTGGCATGCCTTCTTCAAGCTGCTGGCTGTGGTGCTCTTCCTCTTCACCTTTGGGCTG
CTGCCCTGGATCGACAACTTTACACACATTTCGGGGTTCATCAGTGGCCTCTTCCTCTCCTTCACCTTCTAGCCCTACAT
CAGCTTCGGCAAGTTCAGTCTGTACCAGAAATGCTGCCAGATCATCATCTTTCAGATGGTCTTTCTGGGCCTCCTGGCTG
GCCTGGTGGTCCTCTTCTCCTTCTATCCTGTCTGCTGTGAGTGGTGTGAGTTCCTCACCTGCATCCCCTTCACTGACAAG
TTCTGCGAGAAGTACAAACTGGACGCTTAGCTCCAC

Alignment

ORF - retro_pabe_2280 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 86.12 %
• Parental protein coverage: 73.22 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  DGTLRRAQRRSFTPASFLEEDTTDFPDELDTSFFAREGILHEELSTYPDEVFESPSEAALKDWEKAPEQA
          DGTLR.AQRRSFTPAS.L.EDT..FPDELDTSFFA.EGILHEELS.YPDEVFESPSEAALKDWEKA.EQ.
Retrocopy DGTLRQAQRRSFTPASSLAEDT-NFPDELDTSFFAQEGILHEELSIYPDEVFESPSEAALKDWEKAREQE

Parental  DLTGGALDRSELERSHLMLPLERGWRKQKEGAAAPQPKVRLRQEVVSTAGPRRGQRIAVPVRKLFAREKR
          .LTGGALDRSELERSH.MLPLERGWRKQKE...A.QPKVRLRQE.VSTAGP.R.QRIA.PVRKLFAREK.
Retrocopy YLTGGALDRSELERSHPMLPLERGWRKQKEDTVASQPKVRLRQEMVSTAGPPRNQRIAMPVRKLFAREKW

Parental  PYGLGMVGRLTNRTYRKRIDSFVKRQIEDMDDHRPFFTYWLTFVHSLVTILAVCIYGIAPVGFSQHETVD
          .YGL..VG.LT..TY.K.IDSFVKRQIEDMD.HRPFFTYWLTFVHSLVTILA.CIYGI.PVGFSQHETVD
Retrocopy LYGLSKVGPLTIHTYHKHIDSFVKRQIEDMDSHRPFFTYWLTFVHSLVTILALCIYGIMPVGFSQHETVD

Parental  SVLRNRGVYENVKYVQQENFWIGPSSEALIHLGAKFSPCMRQDPQVHSFIRSAREREKHSACCVRNDRSG
          SVL.N..VYENVKYVQQENFWIGPSSEALIHL..KFSPC..QDPQVHSFI...REREKHSACC..N.R.G
Retrocopy SVLWNHWVYENVKYVQQENFWIGPSSEALIHLDDKFSPCICQDPQVHSFICAGREREKHSACCMHNNRLG

Parental  CVQTSEEECSSTLAVWVKWPIHPSAPELAGHKRQFGSVCHQDPRVCDEPSSEDPHEWPEDITKWPICTKN
          C.QTSEEECS..LA.WVKWPIH.SAPELA.HK.QFGSVCH.DPRVCDEPS.EDPHEWPEDITKWPICTK.
Retrocopy CLQTSEEECSFMLAMWVKWPIHSSAPELASHKSQFGSVCH*DPRVCDEPSWEDPHEWPEDITKWPICTKK

Parental  S-AGNHTNHPHMDCVITGRPCCIGTKGRCEITSREYCDFMRGYFHEEATLCSQVHCMDDVCGLLPFLNPE
          ...GNHTN.PH.DC.ITGRPCCIGTKG.CEITSRE.CDFMRGYFHEEATLCSQVHCMDDVCGL.PFLNPE
Retrocopy T>SGNHTNLPHKDCDITGRPCCIGTKGKCEITSREHCDFMRGYFHEEATLCSQVHCMDDVCGLPPFLNPE

Parental  VPDQFYRLWLSLFLHAGILHCLVSICFQMTVLRDLEKLAGWHRIAIIYLLSGVTGNLASAIFLPYRAEVG
          VPDQFY.LWLSLFLH..ILHCLVSICFQMTVLR.LEKLAGWHRIAIIYLLSGVTGN.AS.IFL.YRAEV.
Retrocopy VPDQFYCLWLSLFLHTRILHCLVSICFQMTVLRVLEKLAGWHRIAIIYLLSGVTGNRASVIFLLYRAEVV

Parental  PAGSQFGILACLFVELFQSWQILARPWRAFFKLLAVVLFLFTFGLLPWIDNFAHISGFISGLFLSFAFLP
          P.GS.FGILACLFVELFQSWQIL.RPW.AFFKLLAVVLFLFTFGLLPWIDNF.HISGFISGLFLSF.F.P
Retrocopy PSGS*FGILACLFVELFQSWQILERPWHAFFKLLAVVLFLFTFGLLPWIDNFTHISGFISGLFLSFTF*P

Parental  YISFGKFDLYRKRCQIIIFQVVFLGLLAGLVVLFYFYPVRCEWCEFLTCIPFTDKFCEKYELDAQLH
          YISFGKF.LY.K.CQIIIFQ.VFLGLLAGLVVLF.FYPV.CEWCEFLTCIPFTDKFCEKY.LDA.LH
Retrocopy YISFGKFSLYQKCCQIIIFQMVFLGLLAGLVVLFSFYPVCCEWCEFLTCIPFTDKFCEKYKLDA*LH

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	7.57 RPM
SRP007412_cerebellum	0.00 RPM	4.26 RPM
SRP007412_heart	0.00 RPM	6.50 RPM
SRP007412_kidney	0.00 RPM	9.55 RPM
SRP007412_liver	0.00 RPM	3.73 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_2280 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_2280 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_2280 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 4 parental genes, and 4 retrocopies.

Species	Parental gene accession	Retrocopies number
Homo sapiens	ENSG00000007384	1 retrocopy	retro_hsap_2754,
Gorilla gorilla	ENSGGOG00000028110	1 retrocopy	retro_ggor_1916,
Pongo abelii	ENSPPYG00000006895	1 retrocopy	retro_pabe_2280 ,
Pan troglodytes	ENSPTRG00000007527	1 retrocopy	retro_ptro_1862,