RetrogeneDB ID: retro_pabe_2228

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: 3:88725230..88725569(+)
• Located in intron of: ENSPPYG00000013770

Retrocopy information

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

Parental gene information

• Parental gene symbol: RNF7
• Ensembl ID: ENSPPYG00000014167
• Aliases: None
• Description: ring finger protein 7 [Source:HGNC Symbol;Acc:10070]

Sequence

>retro_pabe_2228
ATGGCCGACGTGGAAGACGGCGAGGAACCCTACGCCCTGACCTCTCACTCCAGGAGCGCGGGCTCCAAGTCGGGAGGCGA
CAAGATGTTCTAGCTCAAGAAGTGGAACGTGGTGGCCATGTGGAGCTAGGACGTGGAGTGCGATACGTGCGCCATCTGCA
GAGTCCAGGTGATGGGTGCCTGTCTCAGATGTCAAGCTGAGAACAAACAAGAGGACTGTGTTGTGGTCATGGGAGAATGT
AATCATTCCTTCCGCAACTGCTGCATGTCCCTGTGGGTGAAACAGAACGATCGCTGCCCTCTCTGCCAGCAGGACTGGGT
GGCCCAAAGAATCGGCAAA

Alignment

ORF - retro_pabe_2228 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 88.5 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 2
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MADVEDGEETCALASHSGSSGSKSGGDKMFSLKKWNAVAMWSWDVECDTCAICRVQVMDACLRCQAENKQ
          MADVEDGEE..AL.SHS.S.GSKSGGDKMF.LKKWN.VAMWS.DVECDTCAICRVQVM.ACLRCQAENKQ
Retrocopy MADVEDGEEPYALTSHSRSAGSKSGGDKMF*LKKWNVVAMWS*DVECDTCAICRVQVMGACLRCQAENKQ

Parental  EDCVVVWGECNHSFHNCCMSLWVKQNNRCPLCQQDWVVQRIGK
          EDCVVV.GECNHSF.NCCMSLWVKQN.RCPLCQQDWV.QRIGK
Retrocopy EDCVVVMGECNHSFRNCCMSLWVKQNDRCPLCQQDWVAQRIGK

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	0.06 RPM	43.85 RPM
SRP007412_cerebellum	0.00 RPM	31.01 RPM
SRP007412_heart	0.00 RPM	20.86 RPM
SRP007412_kidney	0.03 RPM	34.04 RPM
SRP007412_liver	0.03 RPM	25.31 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_2228 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_2228 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_2228 has 1 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_2790

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Parental genes homology:

Parental genes homology involve 19 parental genes, and 42 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000007694	1 retrocopy	retro_cfam_1802,
Choloepus hoffmanni	ENSCHOG00000010742	3 retrocopies	retro_chof_2513, retro_chof_45, retro_chof_518,
Callithrix jacchus	ENSCJAG00000001991	2 retrocopies	retro_cjac_1391, retro_cjac_3943,
Dasypus novemcinctus	ENSDNOG00000005961	3 retrocopies	retro_dnov_1587, retro_dnov_2383, retro_dnov_294,
Homo sapiens	ENSG00000114125	1 retrocopy	retro_hsap_2790,
Gorilla gorilla	ENSGGOG00000001829	1 retrocopy	retro_ggor_1942,
Microcebus murinus	ENSMICG00000001353	1 retrocopy	retro_mmur_1140,
Macaca mulatta	ENSMMUG00000006648	2 retrocopies	retro_mmul_1223, retro_mmul_1440,
Monodelphis domestica	ENSMODG00000021232	1 retrocopy	retro_mdom_201,
Mus musculus	ENSMUSG00000051234	3 retrocopies	retro_mmus_1066, retro_mmus_2450, retro_mmus_3,
Nomascus leucogenys	ENSNLEG00000004646	3 retrocopies	retro_nleu_2038, retro_nleu_2972, retro_nleu_687,
Otolemur garnettii	ENSOGAG00000008659	1 retrocopy	retro_ogar_2433,
Pongo abelii	ENSPPYG00000011861	2 retrocopies	retro_pabe_1986, retro_pabe_1987,
Pongo abelii	ENSPPYG00000014167	2 retrocopies	retro_pabe_1446, retro_pabe_2228 ,
Pan troglodytes	ENSPTRG00000039248	1 retrocopy	retro_ptro_51,
Rattus norvegicus	ENSRNOG00000011663	5 retrocopies	retro_rnor_1858, retro_rnor_1859, retro_rnor_2262, retro_rnor_517, retro_rnor_624,
Ictidomys tridecemlineatus	ENSSTOG00000014964	3 retrocopies	retro_itri_1245, retro_itri_566, retro_itri_567,
Tupaia belangeri	ENSTBEG00000002917	2 retrocopies	retro_tbel_2202, retro_tbel_4027,
Tarsius syrichta	ENSTSYG00000007778	5 retrocopies	retro_tsyr_1222, retro_tsyr_1285, retro_tsyr_1410, retro_tsyr_2117, retro_tsyr_434,