RetrogeneDB ID: retro_itri_471

Retrocopy location

• Organism: Squirrel (Ictidomys tridecemlineatus)
• Coordinates: JH393293.1:17547372..17547764(-)
• Located in intron of: ENSSTOG00000008793

Retrocopy information

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

Parental gene information

• Parental gene symbol: HSDL2
• Ensembl ID: ENSSTOG00000012222
• Aliases: None
• Description: hydroxysteroid dehydrogenase like 2 [Source:HGNC Symbol;Acc:18572]

Sequence

>retro_itri_471
TCATCTGGTGCTATTCTAGAATCTAAAGAAGAGAAGTCAGAGCCACCGTCAAAACTGTGTTCTGGAGCTGTGAAGAAACA
TTTAGAATGAAGGTCTCTCCAATGATGATGATGTGGGAAAGCTACACAAGCCATCTATCAGTTTAAACTCATGGGGTGAC
ACGGTGGCATGTGGTTTCTTGATCTGAAAAACAAGGGCAGGAATGTCATACATGGAGAGCCCTCTGCTAGGGCAGATGTG
GTGATGAGTATGTCTACCAATGATCCTGTCAAAATGTTTTCAGGGAAACCAAAACCAACAATGGCATTCATGTCAGGGAA
AAAGAAGATTAAAGGAAACATGGCCCTAGCAATCAAACACAGAAGCTAATGAATCAAATGCATTCCAGATTG

Alignment

ORF - retro_itri_471 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 70.59 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  SAGAVPEVKEEKPQPQSKAHFGAV-EETFRIVKDSL-SDDVVK-ATQAIYQFELSGEDGGTWFLDLKNRG
          S.GA..E.KEEK..P.SK...GAV.EETFR........DDV.K.ATQAIYQF.L.G..GG.WFLDLKN.G
Retrocopy SSGAILESKEEKSEPPSKLCSGAV<EETFRMKVSPM<DDDVGK<ATQAIYQFKLMG*HGGMWFLDLKNKG

Parental  GNVGHGEPSDKADVVMSMSTDDFVKMFSGKLKPTVAFMSGKLKIKGNMALAIK-LEKLMNQMNSRL
          .NV.HGEPS..ADVVMSMST.D.VKMFSGK.KPT.AFMSGK.KIKGNMALAIK...KLMNQM.SRL
Retrocopy RNVIHGEPSARADVVMSMSTNDPVKMFSGKPKPTMAFMSGKKKIKGNMALAIK<TQKLMNQMHSRL

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_471 retrocopy.

TSS

Ictidomys tridecemlineatus was not studied using FANTOM5 data.

Lab

retro_itri_471 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.

---

Parental genes homology:

Parental genes homology involve 5 parental genes, and 6 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000006832	1 retrocopy	retro_amel_1368,
Canis familiaris	ENSCAFG00000003028	1 retrocopy	retro_cfam_480,
Nomascus leucogenys	ENSNLEG00000016534	1 retrocopy	retro_nleu_649,
Ictidomys tridecemlineatus	ENSSTOG00000012222	1 retrocopy	retro_itri_471 ,
Tupaia belangeri	ENSTBEG00000013420	2 retrocopies	retro_tbel_2324, retro_tbel_3321,