RetrogeneDB ID: retro_pabe_1502

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: 17:43820197..43821256(-)
• Located in intron of: ENSPPYG00000008301

Retrocopy information

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

Parental gene information

• Parental gene symbol: DND1
• Ensembl ID: ENSPPYG00000015863
• Aliases: None
• Description: dead end homolog 1 (zebrafish) [Source:HGNC Symbol;Acc:23799]

Sequence

>retro_pabe_1502
ATGCAGTCCAAACGGGATTGTGAGCTGTGGTGTGAGAGGGTGAAGCCAGAGAACAAGGCGGCGCTGGAGGCGTGGGTCAG
GGAGACAGGCATCCGCCTGGTGCAAGTGAATGGGCAGAGGAAGTATGGCGGGCCACCCCCAGGCTGGGTGGGCAGCCCGC
CGCCAGCTAGGTCAGAGGTGTTCATGGGGCGGCTGCCTCAGGACGTGTACGAGCACCAGCTTATCCCGCTGTTCCAGCGC
GTGGGCCGCCTCTACGAGTTCCGCCTGATGATGACCTTCAGCGGCCTGAACCGCGGCTTCGCCTATGCCGGCTACAGCTC
GCGACGCGGCGCGCAGGCCGCCATCGCCACGCTGCACAACCACCCGCTGCGGCCGTCCTGCCCGCTGCTCGTGTGCCGCA
GCACCGAAAAGTGTGAGCTGACCGTTGACGGCCTGCCGCCGAATCTGACCCGCAGAGCGCTGCTGCTCGCGCTGCAGCCG
CTGGGTCCCGGCCTGCAGGAGGCGCGGCTGCTGCCCAGCCCCGGACCGGCGCCCGGGCAGATCGCTCTGCTCAAATTCAG
CTCGCACCGGGCCGCTGCCATGGCCAAAAAGGCCCTGGAGGAAGGGCAGTCACACCTCTGTGGAGAGCAGGTGGCTGTGG
AGTGGCTCAAGCCAGACCTGAAGCAGCGACTTCGCCAGCAGCTTGTGGGTCCCTCCTTGCGGTCCCCACAGCCAGAGGGC
AGCCAGTTGGCCTTGGCAAGGGACAAGTTAGGGTCCCAAGTGGCTCGGGCTACCCTGTAGTTGCTGTGCCAACGAATGAA
GCTGGGCAGCCCTGTGTTCCTCACCAAGTGTTTGGGCACAGGACCTGCTGGCTGGCACCGCTTCTGGTACTAGGTGGTGA
TTCCTGGGCATCCGGTGCCCTTCAGCGGCCTCATCTGGGTTGTGCTGACCCTAGATGGCCGGGATGGACATGAGGTAGCC
AAGGATGCTGTGTCTGTACGGCTGCTGCAGGCACTCAGTGAGTCTGGGGCCAACCTCCTGTGGTCTGCTGGGGCTGAGGC
AGGTACCATGGTTAAACAG

Alignment

ORF - retro_pabe_1502 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 96.03 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 2
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MQSKRDCELWCERVNPENKAALEAWVRETGIRLVQVNGQRKYGGPPPGWVGSPPPAGSEVFIGRLPQDVY
          MQSKRDCELWCERV.PENKAALEAWVRETGIRLVQVNGQRKYGGPPPGWVGSPPPA.SEVF.GRLPQDVY
Retrocopy MQSKRDCELWCERVKPENKAALEAWVRETGIRLVQVNGQRKYGGPPPGWVGSPPPARSEVFMGRLPQDVY

Parental  EHQLIPLFQRVGRLYEFRLMMTFSGLNRGFAYARYSSRRGAQAAIATLHNHPLRPSCPLLVCRSTEKCEL
          EHQLIPLFQRVGRLYEFRLMMTFSGLNRGFAYA.YSSRRGAQAAIATLHNHPLRPSCPLLVCRSTEKCEL
Retrocopy EHQLIPLFQRVGRLYEFRLMMTFSGLNRGFAYAGYSSRRGAQAAIATLHNHPLRPSCPLLVCRSTEKCEL

Parental  SVDGLPPNLTRSALLLALQPLGPGLQEARLLPSPGPAPGQIALLKFSSHRAAAMAKKALVEGQSHLCGEQ
          .VDGLPPNLTR.ALLLALQPLGPGLQEARLLPSPGPAPGQIALLKFSSHRAAAMAKKAL.EGQSHLCGEQ
Retrocopy TVDGLPPNLTRRALLLALQPLGPGLQEARLLPSPGPAPGQIALLKFSSHRAAAMAKKALEEGQSHLCGEQ

Parental  VAVEWLKPDLKQRLRQQLVDPFLRSPQPEGSQLALARDKLGSQGARATLQLLCQRMKLGSPVFLTKCLGI
          VAVEWLKPDLKQRLRQQLV.P.LRSPQPEGSQLALARDKLGSQ.ARATL.LLCQRMKLGSPVFLTKCLG.
Retrocopy VAVEWLKPDLKQRLRQQLVGPSLRSPQPEGSQLALARDKLGSQVARATL*LLCQRMKLGSPVFLTKCLGT

Parental  GPAGWHRFWYQVVIPGHPVPFSGLIWVVLTLDGRDGHEVAKDAVSVRLLQALSESGANLLCSAGAEAGTM
          GPAGWHRFWY.VVIPGHPVPFSGLIWVVLTLDGRDGHEVAKDAVSVRLLQALSESGANLL.SAGAEAGTM
Retrocopy GPAGWHRFWY*VVIPGHPVPFSGLIWVVLTLDGRDGHEVAKDAVSVRLLQALSESGANLLWSAGAEAGTM

Parental  VKQ
          VKQ
Retrocopy VKQ

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	0.94 RPM
SRP007412_cerebellum	0.00 RPM	0.85 RPM
SRP007412_heart	0.00 RPM	0.15 RPM
SRP007412_kidney	0.00 RPM	0.56 RPM
SRP007412_liver	0.00 RPM	0.24 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_1502 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_1502 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_1502 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 7 parental genes, and 8 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000016345	1 retrocopy	retro_cjac_557,
Homo sapiens	ENSG00000256453	1 retrocopy	retro_hsap_1760,
Macropus eugenii	ENSMEUG00000016276	2 retrocopies	retro_meug_1326, retro_meug_614,
Mus musculus	ENSMUSG00000044595	1 retrocopy	retro_mmus_2548,
Pongo abelii	ENSPPYG00000015863	1 retrocopy	retro_pabe_1502 ,
Pongo abelii	ENSPPYG00000016819	1 retrocopy	retro_pabe_1775,
Rattus norvegicus	ENSRNOG00000016894	1 retrocopy	retro_rnor_2782,