RetrogeneDB ID: retro_ptro_2788

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: 8:105081844..105082393(-)
• Located in intron of: ENSPTRG00000020501

Retrocopy information

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

Parental gene information

• Parental gene symbol: TAGLN2
• Ensembl ID: ENSPTRG00000001533
• Aliases: None
• Description: transgelin 2 [Source:HGNC Symbol;Acc:11554]

Sequence

>retro_ptro_2788
ATGGCCAACAGGGGACCTGCACATGGCCTGAGCCGGGAGGTGCAGCAGAAGATTGAGAAACAGTATGATGCAGATCTGGA
GCAGATCCTGATCCAGTGGATCACCACCCAGTGCCGAAAGGATGTGGGCCGGTCCCAGCCTGGACGCGAGAACTTCCAGA
ACTGGCTCAAGGATGGCACGGTGTTATGTGAGCTCATTAATGCACTGTACCCCAAGGGGCAGGTCCCAGTAAAGAAGATC
CAGGCCTCCACCATGGCCTTCAAGCAGATGGAGCAGATCTCTCAGTTCCTGCAAGCAGCTGAGCGCTATGGCATTAACAC
CACTGACATCTTCCAAACTGTGGACCTCTGGGAAGGAAAGAACATGGCCTGTGTGCAGCGGACGCTGAGGAATCTGGGTG
GGCTGGCAGTAGCCTGGGATGATGGGCTCTTCTCTGCGGATCCCAACTGGTTCCCTAAGAAATCCAAGGAGAATCCTCGG
AACTTCTCGGATAACCAGCTGCAAGAGGGCAAGAACGTGATCGGGCTACAGATGGGGAGCGTCTCAGGC

Alignment

ORF - retro_ptro_2788 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 94.54 %
• Parental protein coverage: 91.96 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MANRGPAYGLSREVQQKIEKQYDADLEQILIQWITTQCRKDVGRPQPGRENFQNWLKDGTVLCELINALY
          MANRGPA.GLSREVQQKIEKQYDADLEQILIQWITTQCRKDVGR.QPGRENFQNWLKDGTVLCELINALY
Retrocopy MANRGPAHGLSREVQQKIEKQYDADLEQILIQWITTQCRKDVGRSQPGRENFQNWLKDGTVLCELINALY

Parental  PEGQAPVKKIQASTMAFKQMEQISQFLQAAERYGINTTDIFQTVDLWEGKNMACVQRTLMNLGGLAVARD
          P.GQ.PVKKIQASTMAFKQMEQISQFLQAAERYGINTTDIFQTVDLWEGKNMACVQRTL.NLGGLAVA.D
Retrocopy PKGQVPVKKIQASTMAFKQMEQISQFLQAAERYGINTTDIFQTVDLWEGKNMACVQRTLRNLGGLAVAWD

Parental  DGLFSGDPNWFPKKSKENPRNFSDNQLQEGKNVIGLQMGTNRG
          DGLFS.DPNWFPKKSKENPRNFSDNQLQEGKNVIGLQMG...G
Retrocopy DGLFSADPNWFPKKSKENPRNFSDNQLQEGKNVIGLQMGSVSG

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	0.13 RPM	20.14 RPM
SRP007412_cerebellum	0.07 RPM	13.87 RPM
SRP007412_heart	0.00 RPM	60.62 RPM
SRP007412_kidney	0.13 RPM	148.54 RPM
SRP007412_liver	0.16 RPM	302.53 RPM
SRP007412_testis	0.00 RPM	7.80 RPM

ChIP-Seq

Pan troglodytes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ptro_2788 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_2788 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_2788 has 1 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_4108

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Parental genes homology:

Parental genes homology involve 14 parental genes, and 40 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,
Pan troglodytes	ENSPTRG00000000979	15 retrocopies	retro_ptro_1061, retro_ptro_1149, retro_ptro_1247, retro_ptro_1447, retro_ptro_1505, retro_ptro_1554, retro_ptro_1871, retro_ptro_215, retro_ptro_2323, retro_ptro_2377, retro_ptro_2831, retro_ptro_2894, retro_ptro_3007, retro_ptro_483, retro_ptro_653,
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,