RetrogeneDB ID: retro_ptro_2931

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: AACZ03153512.1:773..1427(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: SSBP3
• Ensembl ID: ENSPTRG00000000770
• Aliases: None
• Description: single stranded DNA binding protein 3 [Source:HGNC Symbol;Acc:15674]

Sequence

>retro_ptro_2931
ATGTTTGCCAAAGGCAAAGGCTCCTTGGTGCCCTCGGACGGGCAGGCTGGGGAAAAGTTAGCTTTATACGTCTACGAATA
TTTACTGCAGGTAGGAGCACAGAAATCTGCACAGACCTTCTTATCGGAGATTCGCTGGGAAAAAAACATCGCGTTGGGAG
AACCGCCTGGGTTTTTGCACTCGTGGTGGTGTGTATTTTGGGACCTTTACTGTGCAGCTACTAAAAGGAGAGACACTTGT
GAACATTCAAGTGAAGCAAAAGCCTTTCCTGATTCTAGTGCAGCAGCTGCCCTGAGCCCCGTGCTTGGCAACATTCCCCC
CAACAATAGGATGCGGGGAGGCCGAGTCCCGCCAGGTTTCTTTCAGGGTCCTCCGGGGTCACTGCCCTCGCCGCACGCAC
AGCCTCCACCTCACAATCCTAGCAGCATGATGGGACCCCACAGTCAGCCTTTCATGTCACCGCGATACGCAGGCGGCCCC
AGCCCCCCGATCAGAATGGGAAACCAGCCTCCGGGAGGAGTTCCTGGGACACAGCCATTGCTGCCCAATTCCATGGATCC
CGCACGACAACAAGGCCACCCCCACATGGGAGGATCAATGCAGAGAATGAACCCTCCCCGAGGCATGGGGCCCACGGGTC
CCAGCCCACAGAAT

Alignment

ORF - retro_ptro_2931 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 90.83 %
• Parental protein coverage: 63.56 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MFAKGKGSAVPSDGQAREKLALYVYEYLLHVGAQKSAQTFLSEIRWEKNITLGEPPGFLHSWWCVFWDLY
          MFAKGKGS.VPSDGQA.EKLALYVYEYLL.VGAQKSAQTFLSEIRWEKNI.LGEPPGFLHSWWCVFWDLY
Retrocopy MFAKGKGSLVPSDGQAGEKLALYVYEYLLQVGAQKSAQTFLSEIRWEKNIALGEPPGFLHSWWCVFWDLY

Parental  CAAPERRDTCEHSSEAKAFHDYSAAAAPSPVLGNIPPNDGMPGGPIPPGFFQGPPGSQPSPHAQPPPHNP
          CAA..RRDTCEHSSEAKAF.D.SAAAA.SPVLGNIPPN..M.GG..PPGFFQGPPGS.PSPHAQPPPHNP
Retrocopy CAATKRRDTCEHSSEAKAFPDSSAAAALSPVLGNIPPNNRMRGGRVPPGFFQGPPGSLPSPHAQPPPHNP

Parental  SSMMGPHSQPFMSPRYAGGPRPPIRMGNQPPGGVPGTQPLLPNSMDPTRQQGHPNMGGSMQRMNPPRGMG
          SSMMGPHSQPFMSPRYAGGP.PPIRMGNQPPGGVPGTQPLLPNSMDP.RQQGHP.MGGSMQRMNPPRGMG
Retrocopy SSMMGPHSQPFMSPRYAGGPSPPIRMGNQPPGGVPGTQPLLPNSMDPARQQGHPHMGGSMQRMNPPRGMG

Parental  PMGPGPQN
          P.GP.PQN
Retrocopy PTGPSPQN

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	0.04 RPM	24.15 RPM
SRP007412_cerebellum	0.00 RPM	31.44 RPM
SRP007412_heart	0.00 RPM	4.31 RPM
SRP007412_kidney	0.00 RPM	9.81 RPM
SRP007412_liver	0.00 RPM	7.89 RPM
SRP007412_testis	0.00 RPM	7.06 RPM

ChIP-Seq

Pan troglodytes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ptro_2931 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_2931 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_2931 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 6 parental genes, and 13 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000005029	1 retrocopy	retro_cjac_3827,
Homo sapiens	ENSG00000157216	6 retrocopies	retro_hsap_1302, retro_hsap_1384, retro_hsap_2155, retro_hsap_2319, retro_hsap_2539, retro_hsap_3721,
Macropus eugenii	ENSMEUG00000009291	1 retrocopy	retro_meug_1372,
Oryctolagus cuniculus	ENSOCUG00000005903	1 retrocopy	retro_ocun_252,
Pan troglodytes	ENSPTRG00000000770	2 retrocopies	retro_ptro_2618, retro_ptro_2931 ,
Pan troglodytes	ENSPTRG00000010709	2 retrocopies	retro_ptro_1250, retro_ptro_1640,