RetrogeneDB ID: retro_ptro_2925

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: AACZ03150755.1:308..889(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: SCAMP2
• Ensembl ID: ENSPTRG00000007286
• Aliases: None
• Description: None

Sequence

>retro_ptro_2925
AATCCCTTCAAGCCTCCACCAGGCAGTGTGAGGATGCCTAACGTACCCAATACACAACCAGCAATAATGAAACCAACAGA
GAAACATCCAGTTTATACACTGATTGCAAAAAAACATGCATTGGCCCAAGCTGAACTTCTTAAACACCAGGAAGAAGTAG
AAAGAAAAGATGCAGAATTAGTCATCGGGAATGAGAAATGCAAAACCTCACTCAACATGGTAGAAAAAATAATTGGCCAC
TTCTTCTTAGCAATTTTCCTATAGAACCTTGTTTCTATCAGGATTTTTCTGTTGACATTCCTATAGAATTCCAAAAGACA
GTAAAGCTTATATACTACTTGTGGATGTTCCATGCTGTAACACTGTTTCTAAATATCTTCAGATGCTTGTCTTGGTTTTG
TGTTGATTTTGCAAGAGTGGTTGATTTTAGTTTGAGTATCCTGTGGTTCTTGCTTTTTACTCCTTGTTCATTTGTCTGTT
GGTACAGACCACTTTATGGAGCTTTCAGGAGTGACAGTTCATTCAGACTCTTTGTATTCTTCTTCGTCTATATTTGTTAG
TTTGCTGTACATGCATTCCAG

Alignment

ORF - retro_ptro_2925 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 51. %
• Parental protein coverage: 60.18 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  NPFSETNAATTVPVTQLPGSSQPAVLQPSVEPTQPTPQAVVSA-AQAGLLRQQEELDRKAAEL-ERKERE
          NPF.........P....P...QPA...P.......T..A...A.AQA.LL..QEE..RK.AEL....E.E
Retrocopy NPFKPPPGSVRMP--NVP-NTQPAIMKPTEKHPVYTLIAKKHALAQAELLKHQEEVERKDAEL<SHRE*E

Parental  LQNTVANLHVRQNNWPPLPSWCPVKPCFYQDFSTEIPADYQRICKMLYYLWMLHSVTLFLNLLACLAWFS
          .QN.....H.R.NNWP.L.S..P..PCFYQDFS..IP...Q...K..YYLWM.H.VTLFLN...CL.WF.
Retrocopy MQNLTQ--HGRKNNWPLLLSNFPIEPCFYQDFSVDIPIEFQKTVKLIYYLWMFHAVTLFLNIFRCLSWFC

Parental  GNSSKGVDFGLSILWFLIFTPCAFLCWYRPIYKAFRSDNSFSFFVFFFVFFCQIGIYIIQ
          ......VDF.LSILWFL.FTPC.F.CWYRP.Y.AFRSD.SF..FVFFFV..C.......Q
Retrocopy VDFARVVDFSLSILWFLLFTPCSFVCWYRPLYGAFRSDSSFRLFVFFFVYIC*FAVHAFQ

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	0.05 RPM	15.09 RPM
SRP007412_cerebellum	0.04 RPM	14.45 RPM
SRP007412_heart	0.03 RPM	12.18 RPM
SRP007412_kidney	0.00 RPM	63.44 RPM
SRP007412_liver	0.00 RPM	38.30 RPM
SRP007412_testis	0.00 RPM	33.41 RPM

ChIP-Seq

Pan troglodytes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ptro_2925 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_2925 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_2925 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 1 parental gene, and 1 retrocopy.

Species	Parental gene accession	Retrocopies number
Pan troglodytes	ENSPTRG00000007286	1 retrocopy	retro_ptro_2925 ,