RetrogeneDB ID: retro_ptro_778

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: 12:94646047..94647181(-)
• Located in intron of: ENSPTRG00000005302

Retrocopy information

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

Parental gene information

• Parental gene symbol: RBMS2
• Ensembl ID: ENSPTRG00000005104
• Aliases: None
• Description: None

Sequence

>retro_ptro_778
CAGATGGCACCACCTAGCCCAAGCAACAGTACACCTAACAGCAGTAGTGGAAGCAATGGAAATGACCAGCTGAGCAAAAC
CAACCTATACATCCAAGGATTGCAACCAGGCACTACTGACCAAGATCTTGTCAAGCTGTGTCAGCCATATGGCAAGATTG
TTTCCACTAAGGCCATACTGGACAAGACCACAAACAAATGTAAAGGCTATGGCTTTGTAGATTTTGACAGCCCTTCAGCA
GCACAGAAAGCTGTAACAGCACTGAAGGCCAGTGGTGTACAGGCACAGATGGTAAAGCAACAGGAACAGGACCCCACAAA
TTTATACATCTCAAACCTCCCACTGTCAATGGATGAGCAGGAACTGGAGGGGATGCTGAAGCCCTTTGGCCAGGTTATCT
CCACCCGTATCCTTCGAGATACCAGTGGGACCAGCAGAGGTGTTGGCTTTGCAAGGATGGAGTCCACAGAGAAGTGTGAA
GCCATCATCACCCACTTTAATGGAAAATATATTAAGACACCCCCTGGAGTACCAGCCCCATCCGATCCCTTGCTTTGCAA
ATTTGCTGATGGCGGGCCAAAGAAACGACAGAACCAAGGAAAATTTGTGCAAAATGGACGGGCTTGGCCAAGGAATGGAG
ACATGGGCGTCATGGCCTTGACCTATGACCCCACCACAGCTCTTCAGAATGGGTTTTACCCAGCCCCTTGTAACAGCACC
CCCAGCAGGATGCTTGCTCGGTCTGCACTCTCCCCATACCTTTCCTCTCCTGTGTCTTCATATCGGAGAGTGACTCAGAC
ATCTCCTCTACAAGTACCTAACCCATCCTGGATGCACCACCATTCATACCTCATGCAGCCTTCAGGTTCAGTTCTGACAC
CAGGGATGGACCATCCCATTTCTCTCCAGCCTGCCTCCATGATGGGACCCCTTACCCAGCAACTGGGCCATCTCTGCCTC
AGCAGCACAGGCACGTATATGCCGACGGCTGCAGCTATGCAAGGAGCTTACATCTCCCAGTACACCCCTGTGCCTTCTTC
CAGTGTTTCAGTCGAGGAGAGCAGCGGCCAACAGAACCAAGTGGCAGTGGACACACCCTCAGAGCATGGGGTCTATTCTT
TCCAGTTCAACAAG

Alignment

ORF - retro_ptro_778 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 97.62 %
• Parental protein coverage: 92.87 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  QMAPPSPSNSTPNSSSGSNGNDQLSKTNLYIRGLQPGTTDQDLVKLCQPYGKIVSTKAILDKTTNKCKGY
          QMAPPSPSNSTPNSSSGSNGNDQLSKTNLYI.GLQPGTTDQDLVKLCQPYGKIVSTKAILDKTTNKCKGY
Retrocopy QMAPPSPSNSTPNSSSGSNGNDQLSKTNLYIQGLQPGTTDQDLVKLCQPYGKIVSTKAILDKTTNKCKGY

Parental  GFVDFDSPSAAQKAVTALKASGVQAQMAKQQEQDPTNLYISNLPLSMDEQELEGMLKPFGQVISTRILRD
          GFVDFDSPSAAQKAVTALKASGVQAQM.KQQEQDPTNLYISNLPLSMDEQELEGMLKPFGQVISTRILRD
Retrocopy GFVDFDSPSAAQKAVTALKASGVQAQMVKQQEQDPTNLYISNLPLSMDEQELEGMLKPFGQVISTRILRD

Parental  TSGTSRGVGFARMESTEKCEAIITHFNGKYIKTPPGVPAPSDPLLCKFADGGPKKRQNQGKFVQNGRAWP
          TSGTSRGVGFARMESTEKCEAIITHFNGKYIKTPPGVPAPSDPLLCKFADGGPKKRQNQGKFVQNGRAWP
Retrocopy TSGTSRGVGFARMESTEKCEAIITHFNGKYIKTPPGVPAPSDPLLCKFADGGPKKRQNQGKFVQNGRAWP

Parental  RNGDMGVMALTYDPTTALQNGFYPAPYNITPNRMLAQSALSPYLSSPVSSYQRVTQTSPLQVPNPSWMHH
          RNGDMGVMALTYDPTTALQNGFYPAP.N.TP.RMLA.SALSPYLSSPVSSY.RVTQTSPLQVPNPSWMHH
Retrocopy RNGDMGVMALTYDPTTALQNGFYPAPCNSTPSRMLARSALSPYLSSPVSSYRRVTQTSPLQVPNPSWMHH

Parental  HSYLMQPSGSVLTPGMDHPISLQPASMMGPLTQQLGHLSLSSTGTYMPTAAAMQGAYISQYTPVPSSSVS
          HSYLMQPSGSVLTPGMDHPISLQPASMMGPLTQQLGHL.LSSTGTYMPTAAAMQGAYISQYTPVPSSSVS
Retrocopy HSYLMQPSGSVLTPGMDHPISLQPASMMGPLTQQLGHLCLSSTGTYMPTAAAMQGAYISQYTPVPSSSVS

Parental  VEESSGQQNQVAVDAPSEHGVYSFQFNK
          VEESSGQQNQVAVD.PSEHGVYSFQFNK
Retrocopy VEESSGQQNQVAVDTPSEHGVYSFQFNK

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	0.00 RPM	3.11 RPM
SRP007412_cerebellum	0.04 RPM	2.94 RPM
SRP007412_heart	0.12 RPM	9.44 RPM
SRP007412_kidney	0.03 RPM	6.15 RPM
SRP007412_liver	0.00 RPM	1.51 RPM
SRP007412_testis	0.00 RPM	3.37 RPM

ChIP-Seq

Pan troglodytes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ptro_778 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_778 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_778 has 1 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_1143

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Parental genes homology:

Parental genes homology involve 12 parental genes, and 15 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000004054	1 retrocopy	retro_amel_454,
Callithrix jacchus	ENSCJAG00000010803	1 retrocopy	retro_cjac_1022,
Homo sapiens	ENSG00000076067	1 retrocopy	retro_hsap_1143,
Myotis lucifugus	ENSMLUG00000000530	1 retrocopy	retro_mluc_1093,
Mus musculus	ENSMUSG00000040043	1 retrocopy	retro_mmus_1530,
Pan troglodytes	ENSPTRG00000000573	3 retrocopies	retro_ptro_101, retro_ptro_2093, retro_ptro_8,
Pan troglodytes	ENSPTRG00000005104	1 retrocopy	retro_ptro_778 ,
Pan troglodytes	ENSPTRG00000014709	1 retrocopy	retro_ptro_16,
Pteropus vampyrus	ENSPVAG00000007616	2 retrocopies	retro_pvam_1429, retro_pvam_695,
Rattus norvegicus	ENSRNOG00000003076	1 retrocopy	retro_rnor_1374,
Sus scrofa	ENSSSCG00000000402	1 retrocopy	retro_sscr_546,
Tursiops truncatus	ENSTTRG00000002117	1 retrocopy	retro_ttru_715,