RetrogeneDB ID: retro_itri_658

Retrocopy location

• Organism: Squirrel (Ictidomys tridecemlineatus)
• Coordinates: JH393309.1:13517794..13518166(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSSTOG00000024271
• Aliases: None
• Description: None

Sequence

>retro_itri_658
AAAACTCTAAGAGTGAAAAAAGTATAATCATTTAATGGAACAAAAGAAAATATATGCACAGAACTCAAAGCTCTAGTTAA
ACAAGAACCTCTCCAAATAAGATTTGTCAAAACAGTCCTTCAGAAAAGGGAAGATGTACCATCACACAATCAGTACAATT
GCATAATTCTAATAAAAGCAATGAATATTTTTCACCTTAAATCTAATAATCTAGAGAAACTCTTAAAAATCAATCAGCAA
AATCCCCTTGAAAGTATTGAGATCTTTCCTATATACTTAAGATCAATTATGGAGATAAAATATTTGGAATTTTGAGGAAT
CTCTTAATCTCTTGCCAGAGAGAGAAAATCACATAAGGAAGCATAAATAGAA

Alignment

ORF - retro_itri_658 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 54.03 %
• Parental protein coverage: 60. %
• Number of stop codons detected: 4
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  QTLRVEKVPSLDETAENIGAELKAPLKQEPLQVR-VKAVLKKREYGSKYTQNNFITGVRAMNEFCLKPSD
          .TLRV.KV.S...T.ENI..ELKA..KQEPLQ.R.VK.VL.KRE......Q.N.I....AMN.F.LK...
Retrocopy KTLRVKKV*SFNGTKENICTELKALVKQEPLQIRFVKTVLQKREDVPSHNQYNCIILIKAMNIFHLKSNN

Parental  LEQLRKIRQRSPHEDTESFTVYLRSDVEAKSLEVWGSPEALAREKKLRKEAEIE
          LE.L.KI.Q..P.E..E.F..YLRS..E.K.LE..G....LARE.K..KEA.IE
Retrocopy LEKLLKINQQNPLESIEIFPIYLRSIMEIKYLEF*GIS*SLARERKSHKEA*IE

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_658 retrocopy.

TSS

Ictidomys tridecemlineatus was not studied using FANTOM5 data.

Lab

retro_itri_658 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 6 parental genes, and 6 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000019226	1 retrocopy	retro_cjac_408,
Cavia porcellus	ENSCPOG00000000374	1 retrocopy	retro_cpor_805,
Otolemur garnettii	ENSOGAG00000000501	1 retrocopy	retro_ogar_3376,
Rattus norvegicus	ENSRNOG00000002246	1 retrocopy	retro_rnor_2805,
Sus scrofa	ENSSSCG00000008801	1 retrocopy	retro_sscr_326,
Ictidomys tridecemlineatus	ENSSTOG00000024271	1 retrocopy	retro_itri_658 ,