RetrogeneDB ID: retro_pabe_2312

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: 3:73562181..73563048(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: CCDC137
• Ensembl ID: ENSPPYG00000008741
• Aliases: None
• Description: coiled-coil domain containing 137 [Source:HGNC Symbol;Acc:33451]

Sequence

>retro_pabe_2312
ATGGCGCAAGCTGGACATGGAGCAGCGGTGCCCAGGGTGCCGGCGGGTCCTGGGAGTCCCCAGCGGGAGCAGCAGTGGGC
AGCAAGTGCAGCCGCTGGGGAACCAGCGCCCAGCCCCATGGTCCAGGCTTCACAGCAAAGAGGAGAAAGGGAATTGCAAG
CCCAAAACCCAGGACGAACAGGAGATCCCTTTCCGGCTCTGGGAGATTATGAGGAGCCGCCGGGAGATGAAAAATCCGAC
CGGTAACAAGAAGAGGAAGAAAGCGGCCCAGGTGGCCTTCAGAAAGACATTGGAAAAGGAAGCAAAGGGAGTGGAGCCCA
ACATTGCCGTCCCCAAGTTCAAGCAGAGGAAGGGGGAGTCCGACTAGGCCTATATCCAGCGCATGCAGCAAGAGGCCCAG
CACATGCTATTCCTCAGCAAGAGCCAGGCCACCCTGCAGCCAGAGGTCCAGACAGCTCCCAAGGAGAAGTCTGAGCTGTA
AAAAGCAAAAAAAGGGTTCCAGAAGCGACTACTAGATAAAGGCTGGCAGAAAAAGGAGGAAAAGACGGCAGACAGGCTGG
AGCAGGAGTTACTCCGAGACACGGTGAAGTTTGGTAAGGTTGTCCTGCAGGGCCCAGAGCTGACTACCAGGCCCTGGAGG
AGCCTAAGCAAGGACCAGCCTGGCAGGAGATCGCAGATGCTGAGGATGCTTCTGAGCCCCCGCGGTGTATTCCAGCCTCT
GACTGCCTCCCTGGCCTACCAGCGGATTGTGGGGGAGGAGAGAGAGTGGGCCTTGCAAGCCTACAGATGTTGAAGCAGCC
GCGGTGGCTGCATGGGGAGTGACCCCCCCCCCCACTCACTTCCAAGAAGAAGCCAGAGCCACAGCTG

Alignment

ORF - retro_pabe_2312 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 76.11 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 2
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  MARAGRGAAVSRVQAGPGSPRQAR-GRQQVQPLGKQGAAPWPGLRSKEKKKVNCKPKNQDEQEIPFRLRE
          MA.AG.GAAV.RV.AGPGSP.......QQVQPLG.Q..APW..L.SKE.K..NCKPK.QDEQEIPFRL.E
Retrocopy MAQAGHGAAVPRVPAGPGSPQREQ>SGQQVQPLGNQRPAPWSRLHSKEEKG-NCKPKTQDEQEIPFRLWE

Parental  IMRSRQEMKNPISNKKRKKAAQVTFRKTLEKEAKGAEPDITIPKFKQRKGESDGAYIQRMQQEAQHVLFL
          IMRSR.EMKNP..NKKRKKAAQV.FRKTLEKEAKG.EP.I..PKFKQRKGESD.AYIQRMQQEAQH.LFL
Retrocopy IMRSRREMKNPTGNKKRKKAAQVAFRKTLEKEAKGVEPNIAVPKFKQRKGESD*AYIQRMQQEAQHMLFL

Parental  SKNQATRQPEVQAAPKEKSEQKKAKKAFQKRRLDKVRRKKEEKAADRLEQELLRDTVKFGEVVLQPPELT
          SK.QAT.QPEVQ.APKEKSE.......FQKR.LDK...KKEEK.ADRLEQELLRDTVKFG.VVLQ.PELT
Retrocopy SKSQATLQPEVQTAPKEKSELXXXXXGFQKRLLDKGWQKKEEKTADRLEQELLRDTVKFGKVVLQGPELT

Parental  ARPRRSVSKDQPGRRSQMLRMLLSPGGVSQPLTASLARQRIVGEERERAMQAYR-VLKQRRQRLHRE--R
          .RP.RS.SKDQPGRRSQMLRMLLSP.GV.QPLTASLA.QRIVGEERE.A.QAYR..LKQ.R..LH.E...
Retrocopy TRPWRSLSKDQPGRRSQMLRMLLSPRGVFQPLTASLAYQRIVGEEREWALQAYR<MLKQPRW-LHGE*XX

Parental  PHLTSQKKPELQL
          ..LTS.KKPE.QL
Retrocopy XXLTSKKKPEPQL

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	15.54 RPM
SRP007412_cerebellum	0.00 RPM	11.92 RPM
SRP007412_heart	0.00 RPM	4.30 RPM
SRP007412_kidney	0.00 RPM	21.45 RPM
SRP007412_liver	0.00 RPM	7.56 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_2312 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_2312 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_2312 has 3 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_2661
Gorilla gorilla	retro_ggor_1857
Macaca mulatta	retro_mmul_1511

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Parental genes homology:

Parental genes homology involve 10 parental genes, and 12 retrocopies.

Species	Parental gene accession	Retrocopies number
Erinaceus europaeus	ENSEEUG00000014878	1 retrocopy	retro_eeur_523,
Homo sapiens	ENSG00000185298	1 retrocopy	retro_hsap_2661,
Gorilla gorilla	ENSGGOG00000009333	1 retrocopy	retro_ggor_1857,
Macaca mulatta	ENSMMUG00000008831	1 retrocopy	retro_mmul_1511,
Monodelphis domestica	ENSMODG00000002713	1 retrocopy	retro_mdom_1355,
Mus musculus	ENSMUSG00000049957	1 retrocopy	retro_mmus_641,
Nomascus leucogenys	ENSNLEG00000013830	3 retrocopies	retro_nleu_1264, retro_nleu_1530, retro_nleu_586,
Pongo abelii	ENSPPYG00000008741	1 retrocopy	retro_pabe_2312 ,
Pan troglodytes	ENSPTRG00000009767	1 retrocopy	retro_ptro_1793,
Rattus norvegicus	ENSRNOG00000048712	1 retrocopy	retro_rnor_472,