RetrogeneDB ID: retro_pabe_3310

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: 8:30197244..30197661(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: TAGLN2
• Ensembl ID: ENSPPYG00000000648
• Aliases: None
• Description: transgelin 2 [Source:HGNC Symbol;Acc:11554]

Sequence

>retro_pabe_3310
CAATGGATCACCACCCAGTGCCAAAAAGATGTAGGCTGGCCCCAGCTTGGACACGAGAACTTCCAGAACTTCCTCAAGGA
GGGCACAGAGCTATGTGAACTCATTAACGCACTGTGCCCCAAGGGGCAGGCCCCAGTAAAGAAGACCCAGGCCTCTACCA
TGGCCTTAAAGCAGATGGAGCAGATATCTCAGTGCCTGCAAGCAGCTGAGCACTATGGCATTAACACCACTGACATCTTC
CAAACTGTGCACCCCTGGGGAGGAAAGAACGTGGCCTGTGTACGGTGGATCCTGATGAACCTGGGTGGGCTGGTAGTAGC
CCAGGACGATGGGCTCTTCTCTGGGGCTCCCATATGGTTCCCTAAGAAACCCAAGGAGACTCCTTGGAACTTCTCAACCA
GCTACAAGAGGGCAGGA

Alignment

ORF - retro_pabe_3310 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 76.26 %
• Parental protein coverage: 69.85 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  QWITTQCRKDVGRPQPGRENFQNWLKDGTVLCELINALYPEGQAPVKKIQASTMAFKQMEQISQFLQAAE
          QWITTQC.KDVG.PQ.G.ENFQN.LK.GT.LCELINAL.P.GQAPVKK.QASTMA.KQMEQISQ.LQAAE
Retrocopy QWITTQCQKDVGWPQLGHENFQNFLKEGTELCELINALCPKGQAPVKKTQASTMALKQMEQISQCLQAAE

Parental  RYGINTTDIFQTVDLWEGKNMACVQRTLMNLGGLAVARDDGLFSGDPNWFPKKSKENPRNFSDNQLQEG
          .YGINTTDIFQTV..W.GKN.ACV...LMNLGGL.VA.DDGLFSG.P.WFPKK.KE.P.NFS......G
Retrocopy HYGINTTDIFQTVHPWGGKNVACVRWILMNLGGLVVAQDDGLFSGAPIWFPKKPKETPWNFSTSYKRAG

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	39.75 RPM
SRP007412_cerebellum	0.00 RPM	17.27 RPM
SRP007412_heart	0.00 RPM	57.05 RPM
SRP007412_kidney	0.00 RPM	115.19 RPM
SRP007412_liver	0.03 RPM	94.59 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_3310 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_3310 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_3310 has 1 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Macaca mulatta	retro_mmul_2328

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Parental genes homology:

Parental genes homology involve 14 parental genes, and 37 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000002068	1 retrocopy	retro_btau_1701,
Callithrix jacchus	ENSCJAG00000006156	2 retrocopies	retro_cjac_2035, retro_cjac_2444,
Homo sapiens	ENSG00000158710	1 retrocopy	retro_hsap_4108,
Macropus eugenii	ENSMEUG00000006573	9 retrocopies	retro_meug_1092, retro_meug_1242, retro_meug_128, retro_meug_1442, retro_meug_1998, retro_meug_309, retro_meug_483, retro_meug_690, retro_meug_880,
Myotis lucifugus	ENSMLUG00000026228	1 retrocopy	retro_mluc_274,
Macaca mulatta	ENSMMUG00000004705	1 retrocopy	retro_mmul_2328,
Monodelphis domestica	ENSMODG00000010032	1 retrocopy	retro_mdom_1178,
Nomascus leucogenys	ENSNLEG00000013350	1 retrocopy	retro_nleu_575,
Pongo abelii	ENSPPYG00000000648	2 retrocopies	retro_pabe_3310 , retro_pabe_3364,
Pongo abelii	ENSPPYG00000009302	12 retrocopies	retro_pabe_1299, retro_pabe_1397, retro_pabe_1838, retro_pabe_1920, retro_pabe_2171, retro_pabe_2249, retro_pabe_2900, retro_pabe_3512, retro_pabe_3515, retro_pabe_3543, retro_pabe_3823, retro_pabe_407,
Pan troglodytes	ENSPTRG00000001533	1 retrocopy	retro_ptro_2788,
Sus scrofa	ENSSSCG00000006395	2 retrocopies	retro_sscr_312, retro_sscr_313,
Tarsius syrichta	ENSTSYG00000001645	2 retrocopies	retro_tsyr_1911, retro_tsyr_950,
Tursiops truncatus	ENSTTRG00000001814	1 retrocopy	retro_ttru_1614,