RetrogeneDB ID: retro_itri_869

Retrocopy location

• Organism: Squirrel (Ictidomys tridecemlineatus)
• Coordinates: JH393336.1:6070811..6071203(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: CISD2
• Ensembl ID: ENSSTOG00000001408
• Aliases: None
• Description: CDGSH iron sulfur domain 2 [Source:HGNC Symbol;Acc:24212]

Sequence

>retro_itri_869
ATGGCACTAGAAAGCATGGCCACATCATGAAGATATAACTACCTGCTTACTTTAAGTGGCTCCCAGGTCTGGACAGTATT
CTCTGTTTGCTGGCTCAGCAAAAAGTTTCAGAATGGCTTCAAGTCTTGCTTGGTGTTATTGGCTCTAGTTGGCTATCTTG
CACTTTGTTCATTTGTCTCCAGGAAAAACCACAGAAGGACAGATTGATTAATCTCAAAATACAAAAGGAAGACCCCAAAA
TGGCAAATGAAATAAACATTAGGGATTTGTGCTGTGCTACAGCAGCTTATTATAGTGTTGGCACTGGGAGAGTTTTCTGC
CTTCGATGGTTCACAGAATGGACAGGTAAATTGACAAATCATTTCATGGGTATGCTCCTAATGAAGAGGAAG

Alignment

ORF - retro_itri_869 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 53.57 %
• Parental protein coverage: 98.52 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 6

Retrocopy - Parental Gene Alignment:

Parental  MVLESVA-RIVKVQLPAYLKRLPVPESITGF-ARLTVSEWLRLLPFLGV-LALLGYLAVRPFFPKK-KQQ
          M.LES.A..I.K..LPAY.K.LP...SI....A...VSEWL..L..LGV.LAL.GYLA...F...K.K.Q
Retrocopy MALESMA<HIMKI*LPAYFKWLPGLDSILCLLAQQKVSEWLQVL--LGV>LALVGYLALCSFVSRK<KPQ

Parental  KDSLINLKIQKENPKVVNEINIEDLCLTKAAYCR-CWRSKT-FPACDGSHNKH-NELTGDNVGPLILKKK
          KD.LINLKIQKE.PK..NEINI.DLC...AAY...CW.....F.A.DGS.N.....LT....G.L..K.K
Retrocopy KDRLINLKIQKEDPKMANEINIRDLCCATAAYYS<CWHWES<FSAFDGSQNGQ<GKLTNHFMGMLLMKRK

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_869 retrocopy.

TSS

Ictidomys tridecemlineatus was not studied using FANTOM5 data.

Lab

retro_itri_869 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 7 parental genes, and 7 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000010779	1 retrocopy	retro_cfam_1012,
Callithrix jacchus	ENSCJAG00000015530	1 retrocopy	retro_cjac_2668,
Felis catus	ENSFCAG00000028054	1 retrocopy	retro_fcat_1979,
Mus musculus	ENSMUSG00000028165	1 retrocopy	retro_mmus_2257,
Nomascus leucogenys	ENSNLEG00000026930	1 retrocopy	retro_nleu_1331,
Oryctolagus cuniculus	ENSOCUG00000013943	1 retrocopy	retro_ocun_1444,
Ictidomys tridecemlineatus	ENSSTOG00000001408	1 retrocopy	retro_itri_869 ,