RetrogeneDB ID: retro_mmus_1806

Retrocopy location

• Organism: Mouse (Mus musculus)
• Coordinates: 19:7668286..7668790(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSMUSG00000024761
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: Iscu
• Ensembl ID: ENSMUSG00000025825
• Aliases: Iscu, 2310020H20Rik, AA407971, Nifu, Nifun
• Description: IscU iron-sulfur cluster scaffold homolog (E. coli) [Source:MGI Symbol;Acc:MGI:1913633]

Sequence

>retro_mmus_1806
ATGGTGGCGGCCACGGGAGCGGGCCGTCTGAAGCGGGCGGCGTCGGCGCTGCTGCTGCGGAGCCCGCGCCTGCCCGCCCG
GGAGCTGTCGGCTCCGGCCAGGTTCTACCACAAGAAGGTTGTGGATCATTATGAAAACCCTCGGAATGTGGGATCCCTTG
ACAAGACATCTAAAAATGTTGGAACCGGATTGGTGGGGGCTCCGGCATGTGGTGACATCATGAAACTGCAGATCCAGGTG
GATGAAAAGGGGAAGATTGTGGACGCCAGATTCAAAACATTTGGCTGCGGCTCCGCCATTGCCTCCAGCTCCTTAGCCAC
GGAGTGGGTAAAGGGGAAAACGGTGGAGGAAGCCCTGACCATCAAAAACACCGACATCGCCAAGGAGCTCTGCCTGCCGC
CTGTGAAACTGCACTGCTCCATGCTGGCAGAAGACGCCATCAAGGCCGCCCTGGCTGACTACAAACTGAAGCAAGAGTCC
AAGAAGGAAGAGCCAGAGAAGCAG

Alignment

ORF - retro_mmus_1806 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 97.62 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MAAATGAGRLRRAASALLLRSPRLPARELSAPARLYHKKVVDHYENPRNVGSLDKTSKNVGTGLVGAPAC
          M.AATGAGRL.RAASALLLRSPRLPARELSAPAR.YHKKVVDHYENPRNVGSLDKTSKNVGTGLVGAPAC
Retrocopy MVAATGAGRLKRAASALLLRSPRLPARELSAPARFYHKKVVDHYENPRNVGSLDKTSKNVGTGLVGAPAC

Parental  GDVMKLQIQVDEKGKIVDARFKTFGCGSAIASSSLATEWVKGKTVEEALTIKNTDIAKELCLPPVKLHCS
          GD.MKLQIQVDEKGKIVDARFKTFGCGSAIASSSLATEWVKGKTVEEALTIKNTDIAKELCLPPVKLHCS
Retrocopy GDIMKLQIQVDEKGKIVDARFKTFGCGSAIASSSLATEWVKGKTVEEALTIKNTDIAKELCLPPVKLHCS

Parental  MLAEDAIKAALADYKLKQESKKEEPEKQ
          MLAEDAIKAALADYKLKQESKKEEPEKQ
Retrocopy MLAEDAIKAALADYKLKQESKKEEPEKQ

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	0.09 RPM	33.29 RPM
SRP007412_cerebellum	0.04 RPM	49.67 RPM
SRP007412_heart	0.25 RPM	57.19 RPM
SRP007412_kidney	0.96 RPM	107.16 RPM
SRP007412_liver	0.16 RPM	47.38 RPM
SRP007412_testis	0.41 RPM	38.33 RPM

ChIP-Seq

RNA Polymerase II activity near the 5' end of retro_mmus_1806 was not detected

EST

No EST(s) were mapped for retro_mmus_1806 retrocopy.

TSS

No TSS is located nearby retro_mmus_1806 retrocopy 5' end.

Lab

retro_mmus_1806 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmus_1806 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 23 parental genes, and 49 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000016405	3 retrocopies	retro_amel_1338, retro_amel_755, retro_amel_902,
Bos taurus	ENSBTAG00000011787	3 retrocopies	retro_btau_378, retro_btau_646, retro_btau_648,
Canis familiaris	ENSCAFG00000011324	4 retrocopies	retro_cfam_388, retro_cfam_390, retro_cfam_599, retro_cfam_686,
Choloepus hoffmanni	ENSCHOG00000011773	2 retrocopies	retro_chof_229, retro_chof_2698,
Callithrix jacchus	ENSCJAG00000015374	2 retrocopies	retro_cjac_1584, retro_cjac_1644,
Cavia porcellus	ENSCPOG00000010986	1 retrocopy	retro_cpor_1201,
Equus caballus	ENSECAG00000019879	3 retrocopies	retro_ecab_359, retro_ecab_753, retro_ecab_849,
Felis catus	ENSFCAG00000014044	2 retrocopies	retro_fcat_1769, retro_fcat_471,
Homo sapiens	ENSG00000136003	2 retrocopies	retro_hsap_3596, retro_hsap_468,
Gorilla gorilla	ENSGGOG00000011579	2 retrocopies	retro_ggor_2426, retro_ggor_446,
Loxodonta africana	ENSLAFG00000007170	2 retrocopies	retro_lafr_609, retro_lafr_728,
Microcebus murinus	ENSMICG00000013067	4 retrocopies	retro_mmur_1359, retro_mmur_558, retro_mmur_636, retro_mmur_81,
Macaca mulatta	ENSMMUG00000017126	1 retrocopy	retro_mmul_572,
Monodelphis domestica	ENSMODG00000002828	1 retrocopy	retro_mdom_1924,
Mus musculus	ENSMUSG00000025825	2 retrocopies	retro_mmus_1806 , retro_mmus_3317,
Nomascus leucogenys	ENSNLEG00000006797	2 retrocopies	retro_nleu_299, retro_nleu_884,
Oryctolagus cuniculus	ENSOCUG00000016305	1 retrocopy	retro_ocun_637,
Procavia capensis	ENSPCAG00000007604	2 retrocopies	retro_pcap_257, retro_pcap_86,
Pongo abelii	ENSPPYG00000004920	3 retrocopies	retro_pabe_1753, retro_pabe_266, retro_pabe_2956,
Tupaia belangeri	ENSTBEG00000001086	3 retrocopies	retro_tbel_1987, retro_tbel_2588, retro_tbel_545,
Tarsius syrichta	ENSTSYG00000013952	2 retrocopies	retro_tsyr_1484, retro_tsyr_98,
Tursiops truncatus	ENSTTRG00000004036	1 retrocopy	retro_ttru_1720,
Xenopus tropicalis	ENSXETG00000027428	1 retrocopy	retro_xtro_66,