RetrogeneDB ID: retro_ptro_1250

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: 18:4490511..4491213(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: SSBP4
• Ensembl ID: ENSPTRG00000010709
• Aliases: None
• Description: single stranded DNA binding protein 4 [Source:HGNC Symbol;Acc:15676]

Sequence

>retro_ptro_1250
AGGTGGTTGGCGCTGTATGTCTATGAGTACCTGCTGCACATCGGTGCCCAGAAGTCAGCCCAGACCTTCCTGTCTGAGAT
CCGATGGGAGAAGAACATCACGCTGGGGGAGCCCCCCGGGTTCCTGCACTCCTGGTGGTGCGTCTTCTGGGACCTGTACT
GCGCAGCGCCTGACCGAAGAGAGGCCTGCGAGCACTCCGGCGAGGCCAAGGCCTTCCAGGACTATAGCGCTGCAGCCGCC
CCCAGCCCTGTGATGGGGAGTATGGCCCCAGGTGACGCAATGGCCGCAGGCCCCACGGCAGCTGGCTTCTTCCAGGGCCC
CCCCGGCTCCCAGCCATCCCCCCACAACCCCAACGCCCCCGTGATGGGGCCTTACGGTCAGCCCTTCATGTCACTGCGCT
TCCTAGGGGGCCCCCGGCCCACCCTGCGGATGCTGAGTCAGCCTCCCGCAGGCCTCCCCGGCTCCCAGCCCCTCCTCCCT
GGCACCATGGAGCCCTCCCCACGAGCCCAGGGGCATCCGAGCATGGGCGGCCCAATGCAGAGGGTGACGCCTCCTCGCGG
CATTGCCAGCGTGGGGCCCCAGAGCTATGGAGGTGGCATGCGACCCCCACCCAACTCCCTTGCAGGCCCAGGCCTGCCTG
CCATGAACATGGGCCCAGAATTTCGTGGCCCGTGGGCCACCCCCATTGAAAACTCAATCCCC

Alignment

ORF - retro_ptro_1250 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 86.75 %
• Parental protein coverage: 72.45 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  RTLALYVYEYLLHIGAQKSAQTFLFEIRWEKNITLGEPPGFLHSWWCVFWDLYCAAPDRREACEHSGEAK
          R.LALYVYEYLLHIGAQKSAQTFL.EIRWEKNITLGEPPGFLHSWWCVFWDLYCAAPDRREACEHSGEAK
Retrocopy RWLALYVYEYLLHIGAQKSAQTFLSEIRWEKNITLGEPPGFLHSWWCVFWDLYCAAPDRREACEHSGEAK

Parental  AFQDYSAAAAPSPVMGSMAPGDTMAAGPMAAGFFQGPPGSQPSPHNPNAPMMGPHGQPFMSPRFPGGPRP
          AFQDYSAAAAPSPVMGSMAPGD.MAAGP.AAGFFQ................MGP.GQPFMS.RF.GGPRP
Retrocopy AFQDYSAAAAPSPVMGSMAPGDAMAAGPTAAGFFQXXXXXXXXXXXXXXXVMGPYGQPFMSLRFLGGPRP

Parental  TLRMPSQPPAGLPGSQPLLPGAMEPSPRAQGHPSMGGPMQRVTPPRGMASVGPQSYGGGMRPPPNSLAGP
          TLRM.SQPPAGLPGSQPLLPG.MEPSPRAQGHPSMGGPMQRVTPPRG.ASVGPQSYGGGMRPPPNSLAGP
Retrocopy TLRMLSQPPAGLPGSQPLLPGTMEPSPRAQGHPSMGGPMQRVTPPRGIASVGPQSYGGGMRPPPNSLAGP

Parental  GLPAMNMGPGVRGPWASPSGNSIP
          GLPAMNMGP..RGPWA.P..NSIP
Retrocopy GLPAMNMGPEFRGPWATPIENSIP

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	3.29 RPM	41.04 RPM
SRP007412_cerebellum	0.82 RPM	10.75 RPM
SRP007412_heart	0.29 RPM	1.57 RPM
SRP007412_kidney	0.58 RPM	7.64 RPM
SRP007412_liver	0.65 RPM	9.82 RPM
SRP007412_testis	0.00 RPM	1.26 RPM

ChIP-Seq

Pan troglodytes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ptro_1250 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_1250 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_1250 has 1 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_1911

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Parental genes homology:

Parental genes homology involve 4 parental genes, and 6 retrocopies.

Species	Parental gene accession	Retrocopies number
Homo sapiens	ENSG00000130511	1 retrocopy	retro_hsap_1911,
Gorilla gorilla	ENSGGOG00000016931	1 retrocopy	retro_ggor_1759,
Pan troglodytes	ENSPTRG00000000770	2 retrocopies	retro_ptro_2618, retro_ptro_2931,
Pan troglodytes	ENSPTRG00000010709	2 retrocopies	retro_ptro_1250 , retro_ptro_1640,