RetrogeneDB ID: retro_itri_1814

Retrocopy location

• Organism: Squirrel (Ictidomys tridecemlineatus)
• Coordinates: JH393884.1:21713..22331(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSSTOG00000000772
• Aliases: None
• Description: None

Sequence

>retro_itri_1814
GAGTGGTGCCTCATGGAAAGACTCTCCAGGGTCTTTACTGAACTCATTCAAGGATTCGGTTGCCAAGGGGCCCAGGTAGA
AGAAATATGGAGTTTAGAACCTGAGAATTTTTAATAATTAAAACCAGTTCATGGCTTAATTTTTCTTCTCAAGTGGCAGC
TAGAAGAACCAGGATTCACTGTGTTAAGGAGTTCAGACTTACAAGATATATTTCATAAACCCAGTAATTAAAAATGCATG
TGCAACTCAAGCTATTGTCAGTGTGTATTGAACCGTACCCATCAATATGCCCATTTAGGAGAGGCATTATCAGAGTTTAA
AGAATTTTCACAAAGTTTTGATGCAGTTATGAAAGGTTTGGCCCTCAGCAATTTGGATGTGATTCCACAGATACATCACA
GTTTTTTTAGACAGCAAACGTTTGAATTTGATGCAAATACATCAGCCAAAGAAGAAGATGCTTTTCACTTTTTTAGTTAT
GTTCCTGTTAATGGAAGACTGTATGAATTGGATGGACTAAGAGAAGAACCAATTGATTTAGTTGCATACAATCAAGATGA
TCGGATCAGAGCAATATCACCAGTCAGAGAAAAAAGAACACAAAAGTACAGTGAAGAT

Alignment

ORF - retro_itri_1814 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 74.41 %
• Parental protein coverage: 55.91 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  EWCLMESDPGVFTELIKGFGCRGAQVEEIWSLEPENFEKLKPVHGLIFLFKWQPGEEPAGSV-VQDSRLD
          EWCLME....VFTELI.GFGC.GAQVEEIWSLEPENF..LKPVHGLIFL.KWQ..EEP...V.V...RL.
Retrocopy EWCLMERLSRVFTELIQGFGCQGAQVEEIWSLEPENF**LKPVHGLIFLLKWQL-EEPGFTV<VKEFRLT

Parental  T-IFFAKQVINNACATQAIVSV-LLNCTHQDVHLGETLSEFKEFSQSFDAAMKGLALSNSDVIRQVHNSF
          ..I.F...VI.NACATQAIVSV..LN.THQ..HLGE.LSEFKEFSQSFDA.MKGLALSN.DVI.Q.H.SF
Retrocopy R<IYFINPVIKNACATQAIVSV<VLNRTHQYAHLGEALSEFKEFSQSFDAVMKGLALSNLDVIPQIHHSF

Parental  ARQQMFEFDAKTSAKEEDAFHFVSYVPVNGRLYELDGLREGPIDLGACNQDDWISAVRPVIEKRIQNFVF
          .RQQ.FEFDA.TSAKEEDAFHF.SYVPVNGRLYELDGLRE.PIDL.A.NQDD.I.A..PV.EKR.Q....
Retrocopy FRQQTFEFDANTSAKEEDAFHFFSYVPVNGRLYELDGLREEPIDLVAYNQDDRIRAISPVREKRTQKYSE

Parental  D
          D
Retrocopy D

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_1814 retrocopy.

TSS

Ictidomys tridecemlineatus was not studied using FANTOM5 data.

Lab

retro_itri_1814 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 4 parental genes, and 4 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000015914	1 retrocopy	retro_amel_1462,
Monodelphis domestica	ENSMODG00000012129	1 retrocopy	retro_mdom_1507,
Mustela putorius furo	ENSMPUG00000004619	1 retrocopy	retro_mputfur_259,
Ictidomys tridecemlineatus	ENSSTOG00000000772	1 retrocopy	retro_itri_1814 ,