RetrogeneDB ID: retro_ptro_1355

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: 19:21364100..21364415(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: SYNJ2BP
• Ensembl ID: ENSPTRG00000006494
• Aliases: None
• Description: None

Sequence

>retro_ptro_1355
ATGTTTGCACCCGCAGCGATGCGTGCTTTGCGCAAGAATAAGACTCTCCACTACGAAGTCCCCATGTTGTTGCTAATTGT
TGGAGTTTCTTTTGGTGTTCGTGAGTTTTTACAAATCTGACATGATGATGTGAAGATTAAAATTGATCCTGAGTTGGAAA
AAAACTGAAAGCAAATAGTATCATTAGAATCAGAATATGAGAAAATAAAAGACTCCACTTTTGATGACTGGAAGAATATC
CAAGGACCCAAGCCTTGGAAAGATCCTGACCTCCTCCAAGAAAGGAATCCAGAAATCCTTAAGACTAAGACAACC

Alignment

ORF - retro_ptro_1355 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 77.36 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 2
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MFAPAVMRAFRKNKTLRYGVPMLLLIVGGSFGLREFSQIRYDAVKSKMDPELEKKLKENKISLESEYEKI
          MFAPA.MRA.RKNKTL.Y.VPMLLLIVG.SFG.REF.QI..D.VK.K.DPELEK..K....SLESEYEKI
Retrocopy MFAPAAMRALRKNKTLHYEVPMLLLIVGVSFGVREFLQI*HDDVKIKIDPELEKN*KQI-VSLESEYEKI

Parental  KDSKFDDWKNIRGPRPWEDPDLLQGRNPESLKTKTT
          KDS.FDDWKNI.GP.PW.DPDLLQ.RNPE.LKTKTT
Retrocopy KDSTFDDWKNIQGPKPWKDPDLLQERNPEILKTKTT

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	0.09 RPM	10.60 RPM
SRP007412_cerebellum	0.00 RPM	7.78 RPM
SRP007412_heart	0.00 RPM	14.40 RPM
SRP007412_kidney	0.08 RPM	19.06 RPM
SRP007412_liver	0.00 RPM	16.17 RPM
SRP007412_testis	0.00 RPM	18.44 RPM

ChIP-Seq

Pan troglodytes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ptro_1355 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_1355 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_1355 has 2 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_2038
Gorilla gorilla	retro_ggor_1470

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Parental genes homology:

Parental genes homology involve 9 parental genes, and 11 retrocopies.

Species	Parental gene accession	Retrocopies number
Homo sapiens	ENSG00000133983	1 retrocopy	retro_hsap_2038,
Macaca mulatta	ENSMMUG00000011089	2 retrocopies	retro_mmul_1368, retro_mmul_1391,
Nomascus leucogenys	ENSNLEG00000001776	1 retrocopy	retro_nleu_2908,
Otolemur garnettii	ENSOGAG00000028663	1 retrocopy	retro_ogar_3045,
Pongo abelii	ENSPPYG00000005951	2 retrocopies	retro_pabe_1663, retro_pabe_1664,
Pan troglodytes	ENSPTRG00000006494	1 retrocopy	retro_ptro_1355 ,
Rattus norvegicus	ENSRNOG00000047115	1 retrocopy	retro_rnor_1546,
Tarsius syrichta	ENSTSYG00000013313	1 retrocopy	retro_tsyr_1700,
Tursiops truncatus	ENSTTRG00000014791	1 retrocopy	retro_ttru_1513,