RetrogeneDB ID: retro_pabe_1278

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: 15:27346426..27347658(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: REXO4
• Ensembl ID: ENSPPYG00000019735
• Aliases: None
• Description: REX4, RNA exonuclease 4 homolog (S. cerevisiae) [Source:HGNC Symbol;Acc:12820]

Sequence

>retro_pabe_1278
ATGGGGAAGGCGAAGGTCCCCGCCTCCAAGCGCGCCCCGAGCAGCCCCGTGACTAAGCCGGGTCCTGTCAAGACGCTCAC
TGGGAAGAAAAACAAGAAGAAAAAAAGGTTTTGGAAAAGCAAGGCGCAGGAAGTAAGCAAGAAGCCAGGAAGCGGCCCCG
GTGCTGTGGTGCGACCTCCAAAGGCACCAGAAGACTTTTCTCAAAACTGGAAGGCGCTGCAAGAGTGGCTGCTGAAACAA
AAATCTCAGGTCCCAGAAAAGCCTCTTGTCATCTCTCAGATGAGTTCCAAAAAGAAGCCCAAAATTATCCAGCAAAACAA
AAAAGAGACCCCGCCGCAAGTGAAGGGAGAGGAGATGCTGGCAGGAAAAGACCAAGAGGCCAGCAGGGGCTCTGTTCCTT
CAGGCTCCAAGATGGACAAGAAGGCGCCAGTACCTCGCACCAAGGCCAGTGGAGCAGAGCACAGTAAGAAAGGAACCAAG
GAAAGGACAAATGGTGATATTGTTCCAGAACGAGGGGACATCAAGCATAAGAAGCGGAAAGCTGAGGAGGCAGCCCCGGC
CCCACCCACCGAGGAAGACATCTGGTTTGACGACGTGGACCCAGCGGATATCGAAGCTGCCATAGGTCCAGAGGCGGCCA
AGATAGCGAGAAAACAGTTGGGTCAGAGCGAGGGCAGCGTCAGCCTCAGCCTCGTGAAAGAGCAGGCCTTCGGCGGCCTG
ACAAGAGCCTTAGCCTTGGACTGTGAGATGCTGGGCGTGGGCCCTGAGGGGGAGGAGAGCGTGGCCGCCCGTGTGTCCAT
CATGAACCAGGATGGGAAGTGCGTTTATGACAAGTACGTCAAACCAACCGAGCTCGTGACGGACTATAGGACAGCGGTCA
GTGGGATTCAGACTGAGAACCTCAAGCAGGGAGAAGAGCTTGAAGTTGTTCAGAAGGAAGTGGCAGAGATGCTGAAGGGC
AGAATTCTAGTGGGGCATGCTCTGCATAATGACCTAAAGGTACTGTTTCTTGATCACTCAGAAAAGATTCGGGACACACA
GAAATATAAACCTTTCAAGAATCAAGTAAAGAATGGAAGGCCGTCTCCGAGACTACTCTCAGAGAAGATCCTTGGGCTCC
AGGTCCAGCAGGCGGAGACCTGTTCGATTCAGGATGCCCAGGCAGCAATGAGGCTGCACCTCATGGTGAAGGAGTGGAGA
GCATGGCCCAAGATAGGCGCCCCCTGCTGACC

Alignment

ORF - retro_pabe_1278 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 91.28 %
• Parental protein coverage: 97.86 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MGKAKVPASKGASSSPVAKPGPVKTLTRKKNKKKKRFWKSKAQEVSKKPASGPGAVVRPPKAPEDFSQNW
          MGKAKVPASK.A.SSPV.KPGPVKTLT.KKNKKKKRFWKSKAQEVSKKP.SGPGAVVRPPKAPEDFSQNW
Retrocopy MGKAKVPASKRAPSSPVTKPGPVKTLTGKKNKKKKRFWKSKAQEVSKKPGSGPGAVVRPPKAPEDFSQNW

Parental  KALQEWLLKQKSQAPEKPLVISQMGSKKKPKIIQQNKKETSPQVKGEEMPAGKDQEASRGSVPSGSKMDR
          KALQEWLLKQKSQ.PEKPLVISQM.SKKKPKIIQQNKKET.PQVKGEEM.AGKDQEASRGSVPSGSKMD.
Retrocopy KALQEWLLKQKSQVPEKPLVISQMSSKKKPKIIQQNKKETPPQVKGEEMLAGKDQEASRGSVPSGSKMDK

Parental  KAQVPRTKASGAEHNKKGTKERTNGDIVPERGDIKHKKRKAKEAAPAPPTEEDIWFDDVDPADIEAAIGP
          KA.VPRTKASGAEH.KKGTKERTNGDIVPERGDIKHKKRKA.EAAPAPPTEEDIWFDDVDPADIEAAIGP
Retrocopy KAPVPRTKASGAEHSKKGTKERTNGDIVPERGDIKHKKRKAEEAAPAPPTEEDIWFDDVDPADIEAAIGP

Parental  EAAKIARKQLGQSEGSISLSLVKEQAFSGLTRALALDCEMVGVGPKGEESVAARVSIVNQYGKCVYDKYV
          EAAKIARKQLGQSEGS.SLSLVKEQAF.GLTRALALDCEM.GVGP.GEESVAARVSI.NQ.GKCVYDKYV
Retrocopy EAAKIARKQLGQSEGSVSLSLVKEQAFGGLTRALALDCEMLGVGPEGEESVAARVSIMNQDGKCVYDKYV

Parental  KPTEPVTDYRTAVSGIRPENLKQGEVLEVVQKEVAEMLKGRILVGHALHNDLKVLFLDHPKKIRDTQKYK
          KPTE.VTDYRTAVSGI..ENLKQGE.LEVVQKEVAEMLKGRILVGHALHNDLKVLFLDH..KIRDTQKYK
Retrocopy KPTELVTDYRTAVSGIQTENLKQGEELEVVQKEVAEMLKGRILVGHALHNDLKVLFLDHSEKIRDTQKYK

Parental  PFKSQVKSGRPSLRLLSEKILGLQVQQAEHCSIQDAQAAMRLYVTVKKEW-ESMARERRPLLT
          PFK.QVK.GRPS.RLLSEKILGLQVQQAE.CSIQDAQAAMRL...V.KEW.ESMA..RRPLLT
Retrocopy PFKNQVKNGRPSPRLLSEKILGLQVQQAETCSIQDAQAAMRLHLMV-KEW<ESMAQDRRPLLT

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	0.39 RPM	13.82 RPM
SRP007412_cerebellum	0.00 RPM	6.44 RPM
SRP007412_heart	0.09 RPM	3.76 RPM
SRP007412_kidney	0.40 RPM	9.41 RPM
SRP007412_liver	0.06 RPM	4.90 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_1278 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_1278 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_1278 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 4 parental genes, and 5 retrocopies.

Species	Parental gene accession	Retrocopies number
Monodelphis domestica	ENSMODG00000012817	1 retrocopy	retro_mdom_1839,
Mus musculus	ENSMUSG00000052406	2 retrocopies	retro_mmus_1006, retro_mmus_2104,
Nomascus leucogenys	ENSNLEG00000013130	1 retrocopy	retro_nleu_2930,
Pongo abelii	ENSPPYG00000019735	1 retrocopy	retro_pabe_1278 ,