RetrogeneDB ID: retro_pabe_1230

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: 15:32849724..32850316(+)
• Located in intron of: ENSPPYG00000006331

Retrocopy information

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

Parental gene information

• Parental gene symbol: DKFZP459K1410
• Ensembl ID: ENSPPYG00000000787
• Aliases: None
• Description: tropomyosin alpha-3 chain [Source:RefSeq peptide;Acc:NP_001126994]

Sequence

>retro_pabe_1230
ATGGCTGGGATCACCACCATCGAGGCGGTGAAGCGCAAGATCCAGGTTGTGCAGCAGCAGGCAGATGATGCAGAGGAGCG
AGCTGAGCGCTTCCGGCGAGAAGTTGAGGGAGAAAGGCGGGCCCGGGAACAGGCTGAGGCTGAGGTGGCCTCCTTGAACC
TTAGGATCCAGCTGGTTGAAGAGGAGCTGGACCGTGCTCAGGAGCGCCTGGCCACTGCCCTGCAAAAGCTGGAAGAAGCG
GGAAAAGCTGCTGATGAGAGTGAGACAGGTATGAAGGTTTTTGAAAACCAGGCCTTAAAAGATGAAGAAAAGATGGAACT
CCAGGAAATCCAACTCAAAGAAGCTAAGCACATTGCAGAAGAGGAAGGTAGGAAGTATGAAGAGGTGGCTTGTAAGTGGG
TGATCATTGAAGGAGACTTGGAACACACAGAGAATGAGCTGAGCTGGCAGAGTCCCGTTGCCGAGAGATGGATGAGCAGA
TCAGACTGATGGACCAGAACCTGAAGTGTCTGAGTGCTGCTGAAGAAAACTACTCTCAAAAAGAAGACAAATATGAGGAA
GAGATCAAGATTCTACTGATAAACTCAAGGAG

Alignment

ORF - retro_pabe_1230 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 84.0 %
• Parental protein coverage: 79.84 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  MAGITTIEAVKRKIQVLQQQADDAEERAERLQREVEGERRAREQAEAEVASLNRRIQLVEEELDRAQERL
          MAGITTIEAVKRKIQV.QQQADDAEERAER..REVEGERRAREQAEAEVASLN.RIQLVEEELDRAQERL
Retrocopy MAGITTIEAVKRKIQVVQQQADDAEERAERFRREVEGERRAREQAEAEVASLNLRIQLVEEELDRAQERL

Parental  ATALQKLEEAEKAADESERGMKVIENRALKDEEKMELQEIQLKEAKHIAEEADRKYEEVARKLVIIEGDL
          ATALQKLEEA.KAADESE.GMKV.EN.ALKDEEKMELQEIQLKEAKHIAEE..RKYEEVA.K.VIIEGDL
Retrocopy ATALQKLEEAGKAADESETGMKVFENQALKDEEKMELQEIQLKEAKHIAEEEGRKYEEVACKWVIIEGDL

Parental  ERTE-ERAELAESKCSELEEELKNVTNNLKSLEAQAEKYSQKEDKYEEEIKIL-TDKLKE
          E.TE.E.AELAES.C.E..E.......NLK.L.A..E.YSQKEDKYEEEIKIL.TDKLKE
Retrocopy EHTE<E*AELAESRCREMDEQIRLMDQNLKCLSAAEENYSQKEDKYEEEIKIL<TDKLKE

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	0.22 RPM	202.03 RPM
SRP007412_cerebellum	0.12 RPM	68.95 RPM
SRP007412_heart	0.69 RPM	28.30 RPM
SRP007412_kidney	0.99 RPM	97.22 RPM
SRP007412_liver	0.55 RPM	59.12 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_1230 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_1230 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_1230 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 9 parental genes, and 34 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000009747	9 retrocopies	retro_cjac_1232, retro_cjac_1509, retro_cjac_1580, retro_cjac_1910, retro_cjac_2476, retro_cjac_3121, retro_cjac_527, retro_cjac_785, retro_cjac_798,
Gorilla gorilla	ENSGGOG00000012668	3 retrocopies	retro_ggor_1239, retro_ggor_1817, retro_ggor_2621,
Nomascus leucogenys	ENSNLEG00000010990	8 retrocopies	retro_nleu_1133, retro_nleu_2050, retro_nleu_2119, retro_nleu_2141, retro_nleu_2387, retro_nleu_2523, retro_nleu_921, retro_nleu_922,
Otolemur garnettii	ENSOGAG00000025133	1 retrocopy	retro_ogar_62,
Pongo abelii	ENSPPYG00000000787	2 retrocopies	retro_pabe_1230 , retro_pabe_3263,
Pongo abelii	ENSPPYG00000006534	1 retrocopy	retro_pabe_624,
Rattus norvegicus	ENSRNOG00000017441	1 retrocopy	retro_rnor_1524,
Sus scrofa	ENSSSCG00000006556	3 retrocopies	retro_sscr_318, retro_sscr_604, retro_sscr_781,
Ictidomys tridecemlineatus	ENSSTOG00000023525	6 retrocopies	retro_itri_1453, retro_itri_1558, retro_itri_1837, retro_itri_231, retro_itri_674, retro_itri_709,