RetrogeneDB ID: retro_pabe_1083

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: 13_random:877699..878963(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: CASC4
• Ensembl ID: ENSPPYG00000006428
• Aliases: None
• Description: protein CASC4 [Source:RefSeq peptide;Acc:NP_001126659]

Sequence

>retro_pabe_1083
ATGGTGGGTTTCGGGGCCAACCGGTCGGCTGGCCGCCTGCCTTCTCTCGTGCTGGTGGTGCTGCTGGTAGGTAGTGACCG
TCGTCCTCACCTTCAACTGCTGGAGCATCTCTTCCTGCCACGTCCTGCTTCAGGAGGAGGTGGCCGAGCTGCAGGGCCAG
GTCCAGCGCACCGAAGTGGCCCGCGTGCGGCTGGAAAAGCGCAATTCGGACCTCTTGCTGTTGGTGGACACGCACAAGAA
ACAGATCACCAGAAGGAGGCCGACTAGGGCCGCCTCAACAGCCGGCTGCAGGTCAGAGAGGGCCTGGGGAAGAGATGCGA
GGATGACAAAGTTAAACTACAGAACAACACATCGTATCAGATGGCAGACGTACATCATTTAAAGGAGCACCTTGCCGAGC
TTCGTCAGGAGTTTCTTAGACAAGAAGACCGACTTCAGGACTATAGGAAGAACAATACTTACCTTGTGAAGAAGTTAGAA
TATGAAAGTTTTCAGTGCGGACAGCAGATCAAGGAATTCAGAGCACAGCATGAAGAAAATATTAAAAAAGTTAGCAGACC
AGTTTTTACAGTAACAAAAGGAAGAGGCCCTCAAGATTCAGTCAAATGATGGAAAAGAACTGGGTATAAACGATCAAGTA
GTACCTAAAAATATTCCAAAAGTAGCTGAGAATGTTGCAGATAAGAATGAAGAACCCTCAAGCAATCATATTCTACATGG
GAAAGAACAAATCAAAAGAGGTGGTGATGCAGGGATGCCTGGAATAGAAAAGAATGACCTAGCAAAAGTTGATGATCTTC
CCCCTGCTTTAAGGAAACCTCCTATTTCAGTTTCTCAACATGAAAGTCATCAAGCAATCTCCCATCTTCCAACTGGACAA
CCTCTCTCCCCAAATATGCCTCCAGATTCACACATAAACCACAATGGAAACCCTGGTACTTGAAAACAGAAGCCTTCCAG
TCCTCTTCAGCGTTTAATTCCAGGCTCAAACTTGGACAGTGAACCTAGAATTCAAACAGATATACTAAAGCAGGCTACCA
AGGATAGAGTCAGTGAGTTCCATAAATTGAAGCAAAGCCAATTCTTTGATGAGAATGAATCCCCTCTTGATCTGCAGCAT
GGCTCTAAACTGGCGGATTATAATGGGGATGATGGTAACGTAGGTGAGTATGACGCAGACAAGCAGGCTGAGCTGGCTTA
CAATGAGGAAGAAGATGGTGATGGTGGAGCGGAAGATGTCCAAGATGATGAAGAACGAGAGCTT

Alignment

ORF - retro_pabe_1083 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 91.04 %
• Parental protein coverage: 96.33 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  MVGFGANRRAGRLPSLVL-VVLL-VVIVVLAFNYWSISSRHVLLQEEVAELQGQVQRTEVARGRLEKRNS
          MVGFGANR.AGRLPSLVL.V.L..VV.VVL.FN.WSISS.HVLLQEEVAELQGQVQRTEVAR.RLEKRNS
Retrocopy MVGFGANRSAGRLPSLVLVVLLV>VVTVVLTFNCWSISSCHVLLQEEVAELQGQVQRTEVARVRLEKRNS

Parental  DLLLLVDTHKKQID-QKEADYGRLSSRLQAREGLGKRCEDDKVKLQNNISYQMADIHHLKEQLAELRQEF
          DLLLLVDTHKKQI..QKEAD.GRL.SRLQ.REGLGKRCEDDKVKLQNN.SYQMAD.HHLKE.LAELRQEF
Retrocopy DLLLLVDTHKKQIT<QKEAD*GRLNSRLQVREGLGKRCEDDKVKLQNNTSYQMADVHHLKEHLAELRQEF

Parental  LRQEDQLQDYRKNNTYLVKRLEYESFQCGQQIKELRAQHEENIKK-LADQFLQEQKQEAHKIQSNDGKEL
          LRQED.LQDYRKNNTYLVK.LEYESFQCGQQIKE.RAQHEENIKK.LADQFLQ.QK.EA.KIQSNDGKEL
Retrocopy LRQEDRLQDYRKNNTYLVKKLEYESFQCGQQIKEFRAQHEENIKK>LADQFLQ*QKEEALKIQSNDGKEL

Parental  DINDQVVPKNIPKVAENVADKNEEPSSNHIPHGKEQIKRGGDAGMPGIEENDLAKVDDLPPALRKPPISV
          .INDQVVPKNIPKVAENVADKNEEPSSNHI.HGKEQIKRGGDAGMPGIE.NDLAKVDDLPPALRKPPISV
Retrocopy GINDQVVPKNIPKVAENVADKNEEPSSNHILHGKEQIKRGGDAGMPGIEKNDLAKVDDLPPALRKPPISV

Parental  SQHESHQAISHIPTGQPLSPNMPPDSHVNHNGNPGTSKQNPSSPLQRLIPGSNLDSEPRIQTDILKQATK
          SQHESHQAISH.PTGQPLSPNMPPDSH.NHNGNPGT.KQ.PSSPLQRLIPGSNLDSEPRIQTDILKQATK
Retrocopy SQHESHQAISHLPTGQPLSPNMPPDSHINHNGNPGT*KQKPSSPLQRLIPGSNLDSEPRIQTDILKQATK

Parental  DRVSDFHKLKQSRFFDENESPVDPQHGSKLADYNGDDGNVGEYEADKQAELAYNEEEDGDGGEEDVQDDE
          DRVS.FHKLKQS.FFDENESP.D.QHGSKLADYNGDDGNVGEY.ADKQAELAYNEEEDGDGG.EDVQDDE
Retrocopy DRVSEFHKLKQSQFFDENESPLDLQHGSKLADYNGDDGNVGEYDADKQAELAYNEEEDGDGGAEDVQDDE

Parental  EREL
          EREL
Retrocopy EREL

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	47.00 RPM
SRP007412_cerebellum	0.12 RPM	51.68 RPM
SRP007412_heart	0.00 RPM	15.32 RPM
SRP007412_kidney	0.03 RPM	36.56 RPM
SRP007412_liver	0.00 RPM	18.36 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_1083 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_1083 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_1083 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 6 parental genes, and 9 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000006998	4 retrocopies	retro_chof_1422, retro_chof_1445, retro_chof_2453, retro_chof_627,
Homo sapiens	ENSG00000166734	1 retrocopy	retro_hsap_1238,
Nomascus leucogenys	ENSNLEG00000005533	1 retrocopy	retro_nleu_2857,
Oryctolagus cuniculus	ENSOCUG00000005362	1 retrocopy	retro_ocun_1472,
Pongo abelii	ENSPPYG00000006428	1 retrocopy	retro_pabe_1083 ,
Pan troglodytes	ENSPTRG00000007010	1 retrocopy	retro_ptro_852,