RetrogeneDB ID: retro_rnor_1806

Retrocopy location

• Organism: Rat (Rattus norvegicus)
• Coordinates: 3:95351640..95352102(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: Necap1
• Ensembl ID: ENSRNOG00000009236
• Aliases: Necap1, RGD1306053
• Description: Adaptin ear-binding coat-associated protein 1 [Source:UniProtKB/Swiss-Prot;Acc:P69682]

Sequence

>retro_rnor_1806
TTAGATCTGCAAGATCACTTCAAGTGGTAAAGCAGGAAACTAAGATTTCCAAAGGATTGCTTGAAATAGATAATCATCCC
AAGTTCGATTTAGGTTTCAAGGAAGGACAAACCATCAAGTTGAGTACTAGGAACATTACAGACAAGAAAGGAGGTGCTTC
TAAGCCCTGGGCTTCAGGGACAGGGGCCTGAACTTACTCCCACTTTCACCTGGAGGCAAAGTCACTATTCCCACACCACC
CTCCTCAGTTGCCGTCAGCAACCATGTCACCCCACCACCTATTCCAAAATCTAATATGGAGGTAATGATTCAAATATCCT
GTTACATTTGGATTCTCTGGATCCTGCCTTGACTTCAGCACCAGTTCCAGTTTCTATAAGCAATGACTTGTGGGGAAAGT
TCAGCACTTCATCCAGCTCTGTTCCAAACCAGACACCACCGCCATCTAACTGGGTCCAGTTT

Alignment

ORF - retro_rnor_1806 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 74.38 %
• Parental protein coverage: 56.68 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  VSLQDHFKW-VKQETEISKESQEMDSRPKLDLGFKEGQTIKLSIGNITAKKGGTSKPRASGTG-GLSLLP
          ..LQDHFKW.VKQET.ISK...E.D..PK.DLGFKEGQTIKLS..NIT.KKGG.SKP.ASGTG.GL.LLP
Retrocopy LDLQDHFKW<VKQETKISKGLLEIDNHPKFDLGFKEGQTIKLSTRNITDKKGGASKPWASGTG<GLNLLP

Parental  PPPGGKVTIPPPSSSVAISNHVTPPPIPKSN-HGSNDSDILLDLDSPAPVPTSAPAPAPASTSNDLWGDF
          ..PGGKVTIP.P.SSVA.SNHVTPPPIPKSN..G.NDS.ILL.LDS..P..TS..AP.P.S.SNDLWG.F
Retrocopy LSPGGKVTIPTPPSSVAVSNHVTPPPIPKSN<YGGNDSNILLHLDSLDPALTS--APVPVSISNDLWGKF

Parental  STASSSVPNQAPQPSNWVQF
          ST.SSSVPNQ.P.PSNWVQF
Retrocopy STSSSSVPNQTPPPSNWVQF

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
SRP017611_brain	0.00 RPM	141.28 RPM
SRP017611_kidney	0.00 RPM	44.73 RPM
SRP017611_liver	0.00 RPM	22.86 RPM

ChIP-Seq

Rattus norvegicus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_rnor_1806 retrocopy.

TSS

Rattus norvegicus was not studied using FANTOM5 data.

Lab

retro_rnor_1806 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_rnor_1806 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 15 parental genes, and 19 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000016989	1 retrocopy	retro_amel_1016,
Canis familiaris	ENSCAFG00000013930	1 retrocopy	retro_cfam_780,
Choloepus hoffmanni	ENSCHOG00000008087	3 retrocopies	retro_chof_1692, retro_chof_1818, retro_chof_1913,
Dasypus novemcinctus	ENSDNOG00000014778	2 retrocopies	retro_dnov_613, retro_dnov_986,
Homo sapiens	ENSG00000089818	1 retrocopy	retro_hsap_3839,
Gorilla gorilla	ENSGGOG00000010233	1 retrocopy	retro_ggor_2585,
Loxodonta africana	ENSLAFG00000002979	1 retrocopy	retro_lafr_632,
Mustela putorius furo	ENSMPUG00000016742	1 retrocopy	retro_mputfur_361,
Nomascus leucogenys	ENSNLEG00000001743	1 retrocopy	retro_nleu_1974,
Otolemur garnettii	ENSOGAG00000006358	1 retrocopy	retro_ogar_3442,
Pongo abelii	ENSPPYG00000004238	1 retrocopy	retro_pabe_3059,
Pan troglodytes	ENSPTRG00000023277	1 retrocopy	retro_ptro_2615,
Rattus norvegicus	ENSRNOG00000009236	1 retrocopy	retro_rnor_1806 ,
Ictidomys tridecemlineatus	ENSSTOG00000010153	2 retrocopies	retro_itri_1107, retro_itri_740,
Tursiops truncatus	ENSTTRG00000014260	1 retrocopy	retro_ttru_1035,