RetrogeneDB ID: retro_ptro_2053

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: 4:56990914..56991235(-)
• Located in intron of: ENSPTRG00000016149

Retrocopy information

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

Parental gene information

• Parental gene symbol: HMGA1
• Ensembl ID: ENSPTRG00000040884
• Aliases: None
• Description: Pan troglodytes high mobility group AT-hook 1 (HMGA1), mRNA. [Source:RefSeq mRNA;Acc:NM_001246496]

Sequence

>retro_ptro_2053
ATGAGTGCGTCGAGCTTGAAGTCTAGCCAGCCCTTGGCCTCCAAGCAGGAAATGGACAGCACTGAGAAGCGGGGCTGGGG
CAGGCCCCGCAAGCAGCCTCTGGTGAGTTCCGGGACAGCACTGGTAGAGAGTCAGAAGGAGCCCAGTGAAGTGCCAACAC
CTAAGAGACCTTGGGGCCAACCAAAGGGAAGCAAAAACAAGGGAGCTGCCAAGACCCGGAAAACCACCACAACTCCAGGA
AGGAAACCAAGGGGCAGACCCAAAAAACTGGAGAAGGAGGAAGAGGAGGGCATCTGGCAGGAGTCCTCAGAGGAGGAGCA
G

Alignment

ORF - retro_ptro_2053 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 89.72 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MSESSSKSSQPLASKQEKDGTEKRGRGRPRKQPPVSPGTALVGSQKEPSEVPTPKRPRGRPKGSKNKGAA
          MS.SS.KSSQPLASKQE.D.TEKRG.GRPRKQP.VS.GTALV.SQKEPSEVPTPKRP.G.PKGSKNKGAA
Retrocopy MSASSLKSSQPLASKQEMDSTEKRGWGRPRKQPLVSSGTALVESQKEPSEVPTPKRPWGQPKGSKNKGAA

Parental  KTRKTTTTPGRKPRGRPKKLEKEEEEGISQESSEEEQ
          KTRKTTTTPGRKPRGRPKKLEKEEEEGI.QESSEEEQ
Retrocopy KTRKTTTTPGRKPRGRPKKLEKEEEEGIWQESSEEEQ

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	0.46 RPM	59.04 RPM
SRP007412_cerebellum	0.36 RPM	58.65 RPM
SRP007412_heart	0.20 RPM	20.23 RPM
SRP007412_kidney	0.39 RPM	17.89 RPM
SRP007412_liver	0.29 RPM	50.67 RPM
SRP007412_testis	0.21 RPM	41.84 RPM

ChIP-Seq

Pan troglodytes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ptro_2053 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_2053 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_2053 has 1 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Pongo abelii	retro_pabe_2441

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Parental genes homology:

Parental genes homology involve 10 parental genes, and 24 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000001061	1 retrocopy	retro_amel_1637,
Callithrix jacchus	ENSCJAG00000015226	2 retrocopies	retro_cjac_1197, retro_cjac_3158,
Homo sapiens	ENSG00000137309	4 retrocopies	retro_hsap_1175, retro_hsap_2277, retro_hsap_4663, retro_hsap_695,
Myotis lucifugus	ENSMLUG00000010085	2 retrocopies	retro_mluc_1619, retro_mluc_2429,
Macaca mulatta	ENSMMUG00000019529	2 retrocopies	retro_mmul_1276, retro_mmul_2406,
Mus musculus	ENSMUSG00000046711	1 retrocopy	retro_mmus_188,
Nomascus leucogenys	ENSNLEG00000008303	1 retrocopy	retro_nleu_1097,
Pongo abelii	ENSPPYG00000029838	4 retrocopies	retro_pabe_1941, retro_pabe_2441, retro_pabe_3623, retro_pabe_960,
Pan troglodytes	ENSPTRG00000040884	6 retrocopies	retro_ptro_1611, retro_ptro_2053 , retro_ptro_3098, retro_ptro_499, retro_ptro_789, retro_ptro_807,
Rattus norvegicus	ENSRNOG00000000488	1 retrocopy	retro_rnor_164,