RetrogeneDB ID: retro_itri_573

Retrocopy location

• Organism: Squirrel (Ictidomys tridecemlineatus)
• Coordinates: JH393302.1:12243850..12244491(+)
• Located in intron of: ENSSTOG00000001855

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_573
AGGATGAATAAATTCAGTAGCTTGAATGATGATGTCAGTGGGGACCGTGATCAGAATGTAGAAAACAGCACACAGAAAAA
TGGTAGAAATAAAAATGGAATGAGACAAGAGAGCAGCAGCAGAGATGGGTGACTGACCCTGGACCAGCAGAGCATCCTCT
GCAGTACAAACATTTTCTGGTTGCTTCAGGAAGACTCCAAGCTATCCCATCAGCTCAAGAAGCTGTGAACAGATCGTCAA
ACAGATCTGCATCTATGCTTCTGTGGAGCAGTTGTGGAGGCTTTATAGTCACATGGTATGTCCTGGGGACCTGACAGGCA
CAGTGACTTCCATCTCTTCAAAGAAGGAATGAAACACATGTGGGAGGTTAATGCAAATAAAAATGTTGATAAGCAGATTA
TTTTTTGCAGAAGGGCTTGGTCTCCTGTATCTGGGAGAATCTCCTTCTGGCCCTGTTGGGAGAATAGTTCTTAGTTGGGG
AGAAAGTCTATGGGGCTGTGATCTCTGTCCACTTCTAGGGCGGTGTTGTTTCAATATGGAATAACAATGCCAGTGATCAA
GCAGCCACAGCCTGAATCAACGATGTGCTTCAGTATGTGCTTAGCCCACCACCCAACACCATCGTGTACTACAAAGCACA
C

Alignment

ORF - retro_itri_573 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 60.18 %
• Parental protein coverage: 91.95 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  KRKNFSFLKDDDSGDHDQNEENSTQKDGEKEKTERDKSQSSSK-RKAVVPGPAEHPLQYNYTFWYS-RRT
          ....FS.L.DD.SGD.DQN.ENSTQK.G......R....SSS..R....PGPAEHPLQY......S.R.T
Retrocopy RMNKFSSLNDDVSGDRDQNVENSTQKNGRNKNGMRQ--ESSSR<RWVTDPGPAEHPLQYKHFLVAS<RKT

Parental  PGRPTSSQSYEQNIKQIGTFASVEQFWRFYSHMVRPGDLTG-HSDFHLFKEGIKPMWEDDANKNGGKWII
          P..P.SS.S.EQ..KQI...ASVEQ.WR.YSHMV.PGDLTG.HSDFHLFKEG.K.MWE..ANKN..K.II
Retrocopy PSYPISSRSCEQIVKQICIYASVEQLWRLYSHMVCPGDLTG<HSDFHLFKEGMKHMWEVNANKNVDKQII

Parental  R-LRKGLASRCWENLILAMLGEQFMVGEEICGAVVSVRFQEDIISIWNKTASDQATTARIRDTLRRVLNL
          ..L.KGL.S..WENL.LA.LGE.F.VGE...GAV.SV.F.....SIWN..ASDQA.TA.I.D.L..VL..
Retrocopy F<LQKGLVSCIWENLLLALLGE*FLVGEKVYGAVISVHF*GGVVSIWNNNASDQAATA*INDVLQYVLSP

Parental  PPNTIMEYKTH
          PPNTI..YK.H
Retrocopy PPNTIVYYKAH

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_573 retrocopy.

TSS

Ictidomys tridecemlineatus was not studied using FANTOM5 data.

Lab

retro_itri_573 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 ,