RetrogeneDB ID: retro_ptro_2618

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: 7:42344297..42345004(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSPTRG00000034205
• Aliases: None
• Status: KNOWN_PSEUDOGENE

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_2618
ATGTTTGCCAAAGGCAGAGGCTCGGCGGTGCCCTCGGATGGGCAGGCTTGGGAAAAGTTAGCTTTATACGTCTACGAATA
TTTACTGCACGTAAGAGTACAGAAATCTGCAGAGACCTTCTTATCGGAGATTCGATGGGAAAAAACATCACGTTGGGAGA
ACCGCCTGGGTTTTTTCACTCGTGGTGGTGTGTATTTGGGGACCTTTACTGTGCAGCTCCTGAAAGGAGAGACACTTGTG
AACATTCAAGTGAAGCAAAAGCCTTTAATGATTATAGTGCAGCAGCTGCCCCGAGCCCCGTGCTTGGCAACATTCCCCCC
AACGATGGGATGCCGGGAGGCCCCATCCCGCCAGGTTTCTTTCAGGGTCCTCCGGGGTCACAGCCCTCGCCGCACGCACA
GCCTCCACCTCACAATCCTAGCAGCATGATGGGACCCCACAGTCAGCCTTTTATGTCACCGCGATACGTAGGCGGCCCCG
GGCCCCCGATCAGAATGGGAAACCAGCCTCCGGGAGGAGTTCTTGGGACACAGCCATTGCTGCCCAATTCTATGGATCCC
ACAAGACAACAAGGCCACCCCAACATGGGAGGATCAATGCAGAGAATGAACCCTCCCCGAGGCATGGGGCCCATGGGTCC
CGGCCCACAGAATTACGGCAGCGGCATGAGACCACCACCCAACTCCCTCGGCCCGCCATGCCCGGGA

Alignment

ORF - retro_ptro_2618 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 89.08 %
• Parental protein coverage: 69.1 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MFAKGKGSAVPSDGQAREKLALYVYEYLLHVGAQKSAQTFLSEIRWEK-NITLGEPPGFLHSWWCVFWDL
          MFAKG.GSAVPSDGQA.EKLALYVYEYLLHV..QKSA.TFLSEIRWEK.NITLGEPPGF.HSWWCVF.DL
Retrocopy MFAKGRGSAVPSDGQAWEKLALYVYEYLLHVRVQKSAETFLSEIRWEK<NITLGEPPGFFHSWWCVFGDL

Parental  YCAAPERRDTCEHSSEAKAFHDYSAAAAPSPVLGNIPPNDGMPGGPIPPGFFQGPPGSQPSPHAQPPPHN
          YCAAPERRDTCEHSSEAKAF.DYSAAAAPSPVLGNIPPNDGMPGGPIPPGFFQGPPGSQPSPHAQPPPHN
Retrocopy YCAAPERRDTCEHSSEAKAFNDYSAAAAPSPVLGNIPPNDGMPGGPIPPGFFQGPPGSQPSPHAQPPPHN

Parental  PSSMMGPHSQPFMSPRYAGGPRPPIRMGNQPPGGVPGTQPLLPNSMDPTRQQGHPNMGGSMQRMNPPRGM
          PSSMMGPHSQPFMSPRY.GGP.PPIRMGNQPPGGV.GTQPLLPNSMDPTRQQGHPNMGGSMQRMNPPRGM
Retrocopy PSSMMGPHSQPFMSPRYVGGPGPPIRMGNQPPGGVLGTQPLLPNSMDPTRQQGHPNMGGSMQRMNPPRGM

Parental  GPMGPGPQNSIPYSSSSPGTYVGPPGGG
          GPMGPGPQN........P....GPP..G
Retrocopy GPMGPGPQNYGSGMRPPPNS-LGPPCPG

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	5.45 RPM	24.15 RPM
SRP007412_cerebellum	3.44 RPM	31.44 RPM
SRP007412_heart	0.32 RPM	4.31 RPM
SRP007412_kidney	1.36 RPM	9.81 RPM
SRP007412_liver	1.54 RPM	7.89 RPM
SRP007412_testis	0.53 RPM	7.06 RPM

ChIP-Seq

Pan troglodytes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ptro_2618 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_2618 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_2618 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,