RetrogeneDB ID: retro_itri_1432

Retrocopy location

• Organism: Squirrel (Ictidomys tridecemlineatus)
• Coordinates: JH393486.1:198670..199179(+)
• Located in intron of: ENSSTOG00000009541

Retrocopy information

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

Parental gene information

• Parental gene symbol: SOD2
• Ensembl ID: ENSSTOG00000008738
• Aliases: None
• Description: superoxide dismutase 2, mitochondrial [Source:HGNC Symbol;Acc:11180]

Sequence

>retro_itri_1432
CTGCCCAGCAACTACTGCGTCCAGGAGCAGCACGTCAACGCCCAGGTCATGCAGCTGCGCCACAGCAAGCACCATGCGGC
CAATGTGAACAACCTGAACGTGGCGGAGGAGAAAAGTACCGGGAGGCACTGGCCCAGGGAGGTGTTACGGCTCAGGTGGC
CCTTCAACCTGCACTGAAGTTCAATGGCGGAGGTCATGTCAATCACACTATTTTCTGGACAAATCTGAGTCCTAATGGTG
GTGGAGAACCCAAAGGAGAGTTGCTGGAAGCCATCAAATGTGACTTTGGTTCTTTCCACAAGTTTAAAGAGAAGCTGGCA
GCTGTCTCTGTTGGTGTGTGTGTGTGGGGGGGGTCTGGTTGGGGTTGGCTCTGTTTCACTAAGGAGCAGGGACGCTTGCA
GATGGCTGCCTGTTCTAATTAGGATCCTTCGCAAAGAACAACAGGTCTTATTCCACTGCAGGGGATGGATGTCTGGGAGC
ATGCTTATTACCTTCAGCATAAAAACGTC

Alignment

ORF - retro_itri_1432 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 69.59 %
• Parental protein coverage: 74.77 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  LPYDYGALEPHINAQIMEL-HHSKHHAAYVNNLNVTE-DKYREALAKGDVTAQVALQPALKFNGGGHINH
          LP..Y...E.H.NAQ.M.L.H...H.A...N.....E..KYREALA.G.VTAQVALQPALKFNGGGH.NH
Retrocopy LPSNYCVQEQHVNAQVMQLRHSKHHAANVNNLNVAEE<EKYREALAQGGVTAQVALQPALKFNGGGHVNH

Parental  TIFWTNLSPNGGGEPKGELLEAIKRDFGSFDKFKEKLTTVSAGVQGSGW-GW--LGFNKEQGRLQIAACA
          TIFWTNLSPNGGGEPKGELLEAIK.DFGSF.KFKEKL..VS.........GW..L.F.KEQGRLQ.AAC.
Retrocopy TIFWTNLSPNGGGEPKGELLEAIKCDFGSFHKFKEKLAAVSVXXXXXXXSGWGWLCFTKEQGRLQMAACS

Parental  NQDPLQGTTGLIPLLGIDVWEHAYYLQYKNV
          N.DP.Q.TTGLIPL.G.DVWEHAYYLQ.KNV
Retrocopy N*DPSQRTTGLIPLQGMDVWEHAYYLQHKNV

Legend:

• *: Stop codon
• >: Forward frameshift by one nucleotide
• <: Reverse frameshift by one nucleotide

Expression

RNA-Seq

Ictidomys tridecemlineatus was not studied using RNA-Seq expression data.

ChIP-Seq

Ictidomys tridecemlineatus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_itri_1432 retrocopy.

TSS

Ictidomys tridecemlineatus was not studied using FANTOM5 data.

Lab

retro_itri_1432 was not experimentally validated.

Homology

Retrocopy orthology:

Ictidomys tridecemlineatus does not belong to any of the species groups (eutheria, teleost or neognath), studied for retrocopy-based homology. For more information about studied groups, please go to help section.

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Parental genes homology:

Parental genes homology involve 24 parental genes, and 28 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000015466	1 retrocopy	retro_amel_786,
Canis familiaris	ENSCAFG00000000671	1 retrocopy	retro_cfam_1795,
Choloepus hoffmanni	ENSCHOG00000003215	4 retrocopies	retro_chof_1952, retro_chof_1966, retro_chof_2620, retro_chof_937,
Callithrix jacchus	ENSCJAG00000011664	1 retrocopy	retro_cjac_3032,
Dasypus novemcinctus	ENSDNOG00000007907	1 retrocopy	retro_dnov_1653,
Equus caballus	ENSECAG00000011797	2 retrocopies	retro_ecab_70, retro_ecab_840,
Echinops telfairi	ENSETEG00000016400	1 retrocopy	retro_etel_731,
Felis catus	ENSFCAG00000002843	1 retrocopy	retro_fcat_1200,
Homo sapiens	ENSG00000112096	1 retrocopy	retro_hsap_430,
Gorilla gorilla	ENSGGOG00000008212	1 retrocopy	retro_ggor_419,
Myotis lucifugus	ENSMLUG00000012242	1 retrocopy	retro_mluc_528,
Monodelphis domestica	ENSMODG00000007521	1 retrocopy	retro_mdom_373,
Mustela putorius furo	ENSMPUG00000005045	1 retrocopy	retro_mputfur_1382,
Nomascus leucogenys	ENSNLEG00000011061	1 retrocopy	retro_nleu_1023,
Otolemur garnettii	ENSOGAG00000017100	1 retrocopy	retro_ogar_1123,
Pongo abelii	ENSPPYG00000017143	1 retrocopy	retro_pabe_292,
Pan troglodytes	ENSPTRG00000018757	1 retrocopy	retro_ptro_327,
Pteropus vampyrus	ENSPVAG00000005302	1 retrocopy	retro_pvam_288,
Rattus norvegicus	ENSRNOG00000019048	1 retrocopy	retro_rnor_2221,
Sarcophilus harrisii	ENSSHAG00000014795	1 retrocopy	retro_shar_210,
Ictidomys tridecemlineatus	ENSSTOG00000008738	1 retrocopy	retro_itri_1432 ,
Tupaia belangeri	ENSTBEG00000002100	1 retrocopy	retro_tbel_665,
Tarsius syrichta	ENSTSYG00000000457	1 retrocopy	retro_tsyr_183,
Tursiops truncatus	ENSTTRG00000014364	1 retrocopy	retro_ttru_265,