RetrogeneDB ID: retro_itri_1270

Retrocopy location

• Organism: Squirrel (Ictidomys tridecemlineatus)
• Coordinates: JH393420.1:1715567..1716039(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: EIF4E2
• Ensembl ID: ENSSTOG00000003508
• Aliases: None
• Description: eukaryotic translation initiation factor 4E family member 2 [Source:HGNC Symbol;Acc:3293]

Sequence

>retro_itri_1270
ACTCCAGGAGGACCCCAGGCCGTCCCACCAGCTCTCAGAGCTATGAACAGAATATCAAGCAGATTGGCCTCTGTGGAGCA
GTTCTGGAGGTTTTATAGCCACATGGTACGTCCTGGGGACCTGACAGGCCACAGTGACTTCCATGTCTTCAAAAAAGGAA
TTAAACCCATGTGACAAGATGATGCAAATAAAAAGGGTGGCAAGTGGATTGATTATCCAGCTGTGGAAGGGCTTGTCCTC
TCTTTGCTGGGAGAATCTCATCCTGGCTATGCTGGGGGAACAGTTCATGGTGGGGAAGGAGATCTGTGGAGCTGTGGTCT
CTGTCCACTTTCAAGAGGACATTATTTCCATATGGAATAAGACAGCCAGCGACCAAGCAACCACAGCCCAAATCTGTGAT
ACGCTTCCGCGCGTGCTTACCCCACCTCCCAACACCGTTATGGAATACGAAACGCACACCGACAGCATCAAG

Alignment

ORF - retro_itri_1270 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 72.78 %
• Parental protein coverage: 65.68 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  TPGRPTSSQSYEQNIKQIGT-FASVEQFWRFYSHMVRPGDLTGHSDFHLFKEGIKPM-WEDDANKNG-GK
          TPG.P............I....ASVEQFWRFYSHMVRPGDLTGHSDFH.FK.GIKPM...D...K.G...
Retrocopy TPGGPQAVPPALRAMNRISSRLASVEQFWRFYSHMVRPGDLTGHSDFHVFKKGIKPM*QDDANKKGG>SG

Parental  WIIRLRKGLASRCWENLILAMLGEQFMVGEEICGAVVSVRFQEDIISIWNKTASDQATTARIRDTLRRVL
          .II.L.KGL.S.CWENLILAMLGEQFMVG.EICGAVVSV.FQEDIISIWNKTASDQATTA.I.DTL.RVL
Retrocopy LIIQLWKGLSSLCWENLILAMLGEQFMVGKEICGAVVSVHFQEDIISIWNKTASDQATTAQICDTLPRVL

Parental  NLPPNTIMEYKTHTDSIK
          ..PPNT.MEY.THTDSIK
Retrocopy TPPPNTVMEYETHTDSIK

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_1270 retrocopy.

TSS

Ictidomys tridecemlineatus was not studied using FANTOM5 data.

Lab

retro_itri_1270 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 10 parental genes, and 19 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000016456	1 retrocopy	retro_amel_1304,
Canis familiaris	ENSCAFG00000011328	1 retrocopy	retro_cfam_183,
Callithrix jacchus	ENSCJAG00000013786	2 retrocopies	retro_cjac_1061, retro_cjac_2717,
Microcebus murinus	ENSMICG00000015082	2 retrocopies	retro_mmur_806, retro_mmur_975,
Myotis lucifugus	ENSMLUG00000011269	1 retrocopy	retro_mluc_60,
Mustela putorius furo	ENSMPUG00000005206	2 retrocopies	retro_mputfur_110, retro_mputfur_1554,
Otolemur garnettii	ENSOGAG00000009155	1 retrocopy	retro_ogar_104,
Sarcophilus harrisii	ENSSHAG00000013108	1 retrocopy	retro_shar_101,
Ictidomys tridecemlineatus	ENSSTOG00000002230	5 retrocopies	retro_itri_1548, retro_itri_1549, retro_itri_1818, retro_itri_1819, retro_itri_1863,
Ictidomys tridecemlineatus	ENSSTOG00000003508	3 retrocopies	retro_itri_1270 , retro_itri_1370, retro_itri_573,