RetrogeneDB ID: retro_ptro_2418

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: 6:14289079..14289550(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: DSCR3
• Ensembl ID: ENSPTRG00000013900
• Aliases: None
• Description: Down syndrome critical region gene 3 [Source:HGNC Symbol;Acc:3044]

Sequence

>retro_ptro_2418
GTTCACTCCGCTCCTCAGAAGGGGAAGTTTACTCCCAGTCCCGTGGACTTCACGATTACACCTGAAACCTTACAGAACGT
CAAAGAGAGAGCTTTGCTTCCCAAGTTTCTCCTTCGAGGACATCTCAACTCAACAAACTGTGTCATCACACAGCCGCTAA
CGGGAGAGCTGGTGGTGGAGAGCTCGGAAGCCGCCATCAGAAGCGTGGAGCTGCAGCTGGTGCGCGTGGAGACATGCGGG
TGTGCAGAAGGCTATGCCCGCGACGCCACGGAGATTCAGAACATTCAGATCGCCGACGGGGATGTGTGCAGGGGCCTCTC
TGTCCCCATCTACATGGTCTTCCCTAGGCTGTTCACCTGCCCTACACTGGAGACCACCAACTTCAAAGTGGAATTTGAGG
TTAACATCGTGGTGCTTCTTCACCCTGACCACCTCATCACGGAGAACTTCCCGCTGAAGCTCTGCAGGATA

Alignment

ORF - retro_ptro_2418 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 98.09 %
• Parental protein coverage: 58.15 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  VNIQPQKGKFTPSPVDFTITPETLQNVKERALLPKFLLRGHLNSTNCVITQPLTGELVVESSEAAIRSVE
          V...PQKGKFTPSPVDFTITPETLQNVKERALLPKFLLRGHLNSTNCVITQPLTGELVVESSEAAIRSVE
Retrocopy VHSAPQKGKFTPSPVDFTITPETLQNVKERALLPKFLLRGHLNSTNCVITQPLTGELVVESSEAAIRSVE

Parental  LQLVRVETCGCAEGYARDATEIQNIQIADGDVCRGLSVPIYMVFPRLFTCPTLETTNFKVEFEVNIVVLL
          LQLVRVETCGCAEGYARDATEIQNIQIADGDVCRGLSVPIYMVFPRLFTCPTLETTNFKVEFEVNIVVLL
Retrocopy LQLVRVETCGCAEGYARDATEIQNIQIADGDVCRGLSVPIYMVFPRLFTCPTLETTNFKVEFEVNIVVLL

Parental  HPDHLITENFPLKLCRI
          HPDHLITENFPLKLCRI
Retrocopy HPDHLITENFPLKLCRI

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	0.57 RPM	11.62 RPM
SRP007412_cerebellum	0.43 RPM	10.68 RPM
SRP007412_heart	0.99 RPM	12.65 RPM
SRP007412_kidney	1.99 RPM	32.14 RPM
SRP007412_liver	0.95 RPM	19.80 RPM
SRP007412_testis	0.21 RPM	8.22 RPM

ChIP-Seq

Pan troglodytes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ptro_2418 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_2418 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_2418 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 5 parental genes, and 5 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000002626	1 retrocopy	retro_cjac_2878,
Macropus eugenii	ENSMEUG00000007920	1 retrocopy	retro_meug_1828,
Nomascus leucogenys	ENSNLEG00000004717	1 retrocopy	retro_nleu_696,
Pan troglodytes	ENSPTRG00000013900	1 retrocopy	retro_ptro_2418 ,
Rattus norvegicus	ENSRNOG00000001681	1 retrocopy	retro_rnor_1897,