RetrogeneDB ID: retro_itri_420

Retrocopy location

• Organism: Squirrel (Ictidomys tridecemlineatus)
• Coordinates: JH393290.1:3727149..3727668(-)
• Located in intron of: ENSSTOG00000001232

Retrocopy information

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

Parental gene information

• Parental gene symbol: EIF3H
• Ensembl ID: ENSSTOG00000001403
• Aliases: None
• Description: eukaryotic translation initiation factor 3, subunit H [Source:HGNC Symbol;Acc:3273]

Sequence

>retro_itri_420
TCTCTCTCATTAAAGGCAAACTGACTCCTAAAGTTGGAAGTTTTGGCAATGAAGAATTTTCCCCCTGAAATATTTTTAAA
AAGGAAGATAGCATCCTTTGAGCACATGTTTGAAGAAGTACCAATTTTAACTAAAAATTTATATCTGATCAATGTCCTAA
TTTGGGAGTTTGAGAAGTTTGTTATAGCAGATAAATATGAATTGCTCAGCCTTGCTAGCAGCAAACATTTGGGGAAGAAT
TACAATTGCTAAAGGACAAAGGAAATGAAATAAGTCAAGACATAGTTAAATATAATATGCACACAAGGAATGCTAGCAAA
CAGTAGCAATAGAAACATCAATATCACCAAGGTCACCAGCTGGAGAATATGTAGCACCAGAGACAGGAGAATACAGCTCC
TCCAAAGTCCTGTCCAAACTCTTCAAGCCATCCAGGCCTCTTCCATGATGGATTTGATTCTCACTGCAGACCAAATTAAC
ACTTACAACCAGAACATCTAAGAACTCACTGCCCAAAAT

Alignment

ORF - retro_itri_420 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 61.33 %
• Parental protein coverage: 50.28 %
• Number of stop codons detected: 5
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  SLSLKAYRLTPKLMEVCKEKDFSPEALKKANI-TFEHMFEEVPIVIKNSHLINVLMWELEKKSAVADKHE
          SLSLKA..L.....EV...K.F.PE...K..I..FEHMFEEVPI..KN..LINVL.WE.EK....ADK.E
Retrocopy SLSLKAN*LLK--LEVLAMKNFPPEIFLKRKIASFEHMFEEVPILTKNLYLINVLIWEFEK-FVIADKYE

Parental  LLSLASSNHLGKN-LQLLMDRVDEMSQDIVKYNTYMRNTSKQQQQKHQYQQRRQQENMQRQSRGEPPLPE
          LLSLASS.HLGKN.LQLL.D...E.SQDIVKYN...RN.SKQ.Q.KHQY.Q..Q.ENM..Q.R.E...P.
Retrocopy LLSLASSKHLGKN<LQLLKDKGNEISQDIVKYNMHTRNASKQ*Q*KHQYHQGHQLENM*HQ-RQENTAPP

Parental  ED-LSKLFKP-LQAPARMDSLLIAGQINTYCQNIKEFTAQN
          ...LSKLFKP..QA...MD..L.A.QINTY.QNI.E.TAQN
Retrocopy KS<LSKLFKP<IQASSMMDLILTADQINTYNQNI*ELTAQN

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_420 retrocopy.

TSS

Ictidomys tridecemlineatus was not studied using FANTOM5 data.

Lab

retro_itri_420 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 11 parental genes, and 14 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000000816	1 retrocopy	retro_cfam_2073,
Callithrix jacchus	ENSCJAG00000005910	1 retrocopy	retro_cjac_3023,
Echinops telfairi	ENSETEG00000000324	1 retrocopy	retro_etel_24,
Macropus eugenii	ENSMEUG00000015663	4 retrocopies	retro_meug_1223, retro_meug_1244, retro_meug_1790, retro_meug_376,
Monodelphis domestica	ENSMODG00000004154	1 retrocopy	retro_mdom_1243,
Mus musculus	ENSMUSG00000022312	1 retrocopy	retro_mmus_1668,
Oryctolagus cuniculus	ENSOCUG00000007534	1 retrocopy	retro_ocun_608,
Otolemur garnettii	ENSOGAG00000008905	1 retrocopy	retro_ogar_2043,
Sorex araneus	ENSSARG00000009067	1 retrocopy	retro_sara_69,
Sarcophilus harrisii	ENSSHAG00000014977	1 retrocopy	retro_shar_561,
Ictidomys tridecemlineatus	ENSSTOG00000001403	1 retrocopy	retro_itri_420 ,