RetrogeneDB ID: retro_ptro_223

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: 1:151212799..151213642(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: SLC25A38
• Ensembl ID: ENSPTRG00000014772
• Aliases: None
• Description: None

Sequence

>retro_ptro_223
TTACATCTGGTGATCAAGGCTTTCCTGTGTGGCTCCATCAGTGGAACCTGCTCTACCCTCCTTTTCCAACCTCTGGATCT
CCTTAAAACACGCCTGCAAACCCTCCAGCCCTCAGATCATGGGTCTAGACGTGTTGGGATGTTGGCTGTACTCTTGAAGG
TGGTTCACATGGAGAGTCTTTTGGGCCTTTGGAAAGGGATGTCCCCTTCCATTGTGAGATGTGTCCCTGGCGTTGGAATC
TACTTTGGCACTCTCTAATCTTTGAAGCGGTATTTCTTGCGAGGCCATCCCCCAACCGCCCTGGAGTCAATCATGCTGGG
GGTGGGCTCTCTCTCTGTTGCAGGGGTCTGTATGTTACCCATCACTGTAATCAAGATGTGCTATGAGAGTGGGAAATATG
GCTATGAGAGTATCTACGCTGCCCTGAGGAGCATCTATCGCACTGAGGGGCACCGGGGCCTCTTCAGTGGCCTGACAGCA
ACTCTCCTTCGAGATGTGCCCTTTTCAGGAAACTACCTGATGTTTTACAACCAGACCAAAAACATAGTGCCCCATGAGCA
GGTGGATGCAACTTTTATTCCTATTACAAATTTCAGCTGTGGGATATTTGCTGATATTCTCGCCTCACTGGTAACTCAAC
CTGTGGATGTTATCAAAACTCATATGCAGCTTTACCCACTGAAGTTTCAATGGATTGGCCAAGCAGTGACACTTATTTTC
AAAGACTATGGACTACGTGGCTTATTCCAAGGTGGCATCCCCCGAGCCCTCTGCAGAACTCTAATGGCAGCAATGGTGTA
GATGGTGTATGAAGAAATGATGGCCAAGATGGGCCTGAAGTCC

Alignment

ORF - retro_ptro_223 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 91.81 %
• Parental protein coverage: 92.43 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  LHPVIKAFLCGSISGTCSTLLFQPLDLLKTRLQTLQPSDHGSRRVGMLAVLLKVVRTESLLGLWKGMSPS
          LH.VIKAFLCGSISGTCSTLLFQPLDLLKTRLQTLQPSDHGSRRVGMLAVLLKVV..ESLLGLWKGMSPS
Retrocopy LHLVIKAFLCGSISGTCSTLLFQPLDLLKTRLQTLQPSDHGSRRVGMLAVLLKVVHMESLLGLWKGMSPS

Parental  IVRCVPGVGIYFGTLYSLKQYFLRGHPPTALESVMLGVGSRSVAGVCMSPITVIKTRYESGKYGYESIYA
          IVRCVPGVGIYFGTL.SLK.YFLRGHPPTALES.MLGVGS.SVAGVCM.PITVIK..YESGKYGYESIYA
Retrocopy IVRCVPGVGIYFGTL*SLKRYFLRGHPPTALESIMLGVGSLSVAGVCMLPITVIKMCYESGKYGYESIYA

Parental  ALRSIYHSEGHRGLFSGLTATLLRDAPFSGIYLMFYNQTKNIVPHDQVDATLIPITNFSCGIFAGILASL
          ALRSIY..EGHRGLFSGLTATLLRD.PFSG.YLMFYNQTKNIVPH.QVDAT.IPITNFSCGIFA.ILASL
Retrocopy ALRSIYRTEGHRGLFSGLTATLLRDVPFSGNYLMFYNQTKNIVPHEQVDATFIPITNFSCGIFADILASL

Parental  VTQPADVIKTHMQLYPLKFQWIGQAVTLIFKDYGLRGFFQGGIPRALRRTLMAAMAWTVYEEMMAKMGLK
          VTQP.DVIKTHMQLYPLKFQWIGQAVTLIFKDYGLRG.FQGGIPRAL.RTLMAAM...VYEEMMAKMGLK
Retrocopy VTQPVDVIKTHMQLYPLKFQWIGQAVTLIFKDYGLRGLFQGGIPRALCRTLMAAMV*MVYEEMMAKMGLK

Parental  S
          S
Retrocopy S

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	0.02 RPM	20.02 RPM
SRP007412_cerebellum	0.04 RPM	20.36 RPM
SRP007412_heart	0.00 RPM	11.78 RPM
SRP007412_kidney	0.08 RPM	37.21 RPM
SRP007412_liver	0.03 RPM	40.49 RPM
SRP007412_testis	0.00 RPM	23.29 RPM

ChIP-Seq

Pan troglodytes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ptro_223 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_223 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_223 has 2 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_266
Gorilla gorilla	retro_ggor_315

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Parental genes homology:

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

Species	Parental gene accession	Retrocopies number
Homo sapiens	ENSG00000144659	1 retrocopy	retro_hsap_266,
Gorilla gorilla	ENSGGOG00000013530	1 retrocopy	retro_ggor_315,
Nomascus leucogenys	ENSNLEG00000005614	1 retrocopy	retro_nleu_868,
Pan troglodytes	ENSPTRG00000014772	1 retrocopy	retro_ptro_223 ,
Rattus norvegicus	ENSRNOG00000018552	1 retrocopy	retro_rnor_2942,
Tupaia belangeri	ENSTBEG00000015842	1 retrocopy	retro_tbel_1400,