RetrogeneDB ID: retro_pabe_1593

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: 18:38632003..38632927(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: UFD1L
• Ensembl ID: ENSPPYG00000011580
• Aliases: None
• Description: ubiquitin fusion degradation 1 like (yeast) [Source:HGNC Symbol;Acc:12520]

Sequence

>retro_pabe_1593
ATGTTCTCTTTCAACATGTTCAACCACCCAATTCCCAGGGTCTTCCAAAACCACTTCTCCACACAGTACCGCTGCTTCTC
TGTGTCCATGCTAGCAGGGCCTAATGACAGGTCAGATGTGGAGAAAGGAGGGAAGATAATTATGCTGCCCTCAGCCCTGG
ACCAACTCAGCCAACTTAACATTACCTATCCCATGCTGTTCAAACTGACCAATAAGAATTTGGACCGCATGACGCACTGT
GGCGTGCTGGAGTTTGTGGCTGATGAGGGTATCTGCTACCTCCCACACTGGATGATGCCGAACTTGCTCTTGGAAGAAGG
CAGCCTGGTCCAGGTGGACAGTGTCAACCTTCAAGTAGCCACCTACTCCAAATTCCAGCCTCAGAGCCCTGACTTCCTGG
ACATCACCAACCCCAAAGCTGTATTAGAATACACACTTAGGAACTTTGCCTGTCTGACCACCGGGAATGTGACTGCCATC
AACTGTAATGAAAAGATCTACGAACTTGAACTGCGTGTGATGGAAACCAAACCCAACAAGGTAGTGTCCATCATTGAGTG
TGACAGGAACGTGGACTTTGATGCTCCCCTGGGCTACAAAGAACCCAAAAGACAAGTCCAGCATGAGGAGTCGACAGAAG
GTGAAGCCGACCACAGTGGCTATGCTGGAGAGCTGGGCTTCCGTGCCTTCTCGTGCTCTGGCAATAGACTTGATGGAAAG
AAGAAAGGGGTGGAGCCCACCCCCTCCCCAATCAAGCCTGGAGACATTAAAAAAGGAATTCCCAATTATGAATTTAAACT
TGGTAAGATACCTTTCATCAGAAATGCATGTCCCCTTGTCAAAAAGGTTGAAGAGGATGAAGCTGGAGGCAGATTCGTCG
CTTTCTCTGGAGGACAGTCGTTGAGTAAAAAGGGAAGAAAGCCC

Alignment

ORF - retro_pabe_1593 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 91.26 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MFSFNMFDHPIPRVFQNRFSTQYRCFSVSMLAGPNDRSDVEKGGKIIMPPSALDQLSRLNITYPMLFKLT
          MFSFNMF.HPIPRVFQN.FSTQYRCFSVSMLAGPNDRSDVEKGGKIIM.PSALDQLS.LNITYPMLFKLT
Retrocopy MFSFNMFNHPIPRVFQNHFSTQYRCFSVSMLAGPNDRSDVEKGGKIIMLPSALDQLSQLNITYPMLFKLT

Parental  NKNSDRMTHCGVLEFVADEGICYLPHWMMQNLLLEEGGLVQVESVNLQVATYSKFQPQSPDFLDITNPKA
          NKN.DRMTHCGVLEFVADEGICYLPHWMM.NLLLEEG.LVQV.SVNLQVATYSKFQPQSPDFLDITNPKA
Retrocopy NKNLDRMTHCGVLEFVADEGICYLPHWMMPNLLLEEGSLVQVDSVNLQVATYSKFQPQSPDFLDITNPKA

Parental  VLENALRNFACLTTGDVIAINYNEKIY--ELRVMETKPDKAVSIIECDMNVDFDAPLGYKEPERQVQHEE
          VLE..LRNFACLTTG.V.AIN.NEKIY..ELRVMETKP.K.VSIIECD.NVDFDAPLGYKEP.RQVQHEE
Retrocopy VLEYTLRNFACLTTGNVTAINCNEKIYELELRVMETKPNKVVSIIECDRNVDFDAPLGYKEPKRQVQHEE

Parental  STEGEADHSGYAGELGFRAFSGSGNRLDGKKKGVEPSPSPIKPGDIKRGIPNYEFKLGKITFIRNSRPLV
          STEGEADHSGYAGELGFRAFS.SGNRLDGKKKGVEP.PSPIKPGDIK.GIPNYEFKLGKI.FIRN..PLV
Retrocopy STEGEADHSGYAGELGFRAFSCSGNRLDGKKKGVEPTPSPIKPGDIKKGIPNYEFKLGKIPFIRNACPLV

Parental  KKVEEDEAGGRFVAFSGEGQSLRKKGRKP
          KKVEEDEAGGRFVAFSG.GQSL.KKGRKP
Retrocopy KKVEEDEAGGRFVAFSG-GQSLSKKGRKP

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	0.17 RPM	13.44 RPM
SRP007412_cerebellum	0.00 RPM	21.04 RPM
SRP007412_heart	0.09 RPM	10.17 RPM
SRP007412_kidney	0.23 RPM	19.59 RPM
SRP007412_liver	0.24 RPM	23.50 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_1593 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_1593 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_1593 has 3 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_1929
Gorilla gorilla	retro_ggor_175
Macaca mulatta	retro_mmul_1347

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Parental genes homology:

Parental genes homology involve 7 parental genes, and 7 retrocopies.

Species	Parental gene accession	Retrocopies number
Felis catus	ENSFCAG00000004294	1 retrocopy	retro_fcat_604,
Homo sapiens	ENSG00000070010	1 retrocopy	retro_hsap_1929,
Gorilla gorilla	ENSGGOG00000004104	1 retrocopy	retro_ggor_175,
Myotis lucifugus	ENSMLUG00000002466	1 retrocopy	retro_mluc_1244,
Macaca mulatta	ENSMMUG00000031106	1 retrocopy	retro_mmul_1347,
Pongo abelii	ENSPPYG00000011580	1 retrocopy	retro_pabe_1593 ,
Pteropus vampyrus	ENSPVAG00000006417	1 retrocopy	retro_pvam_1349,