RetrogeneDB ID: retro_shar_101

Retrocopy location

• Organism: Tasmanian devil (Sarcophilus harrisii)
• Coordinates: GL861608.1:2756982..2757417(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSSHAG00000017500
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: EIF4E2
• Ensembl ID: ENSSHAG00000013108
• Aliases: None
• Description: eukaryotic translation initiation factor 4E family member 2 [Source:HGNC Symbol;Acc:3293]

Sequence

>retro_shar_101
ATGAACAAGTTCGACGCCTTGAAAGATGATGACAGTGGGGACCATGATCAGAATGAAGAAAAGAGCACACAGAAAGACGG
TGAGAAGGAAAAAAGTGAGCAAGAAAAAAGTCAGAGCAGCAGCAAGAGGAAGGCTGTGGTCCCTGGGCCTGCAGAACACC
TGCTGCAGTACAACTACACTTTCTGGTACTCCCGGAGGACACCAGGCTGGCCGACCAGCTCACAGAGCTACAAGCAGAAC
ATTAAGCAGATTGGTACATTCACCTCCGTGGAGCCATTCTGGAGGTTTTATAGCCACATGGTACGTCTCAGGGACCTGAC
AGGCCATAGTGACTTCCATCTCTTCAAAGAGGGGATCAAACCCATGGGGGAGGATGATGCAAATAAAAATGGCAGCAAAT
GGATTATTCGACTCTGCAAGGGCTTAGCATCATGA

Alignment

ORF - retro_shar_101 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 89.36 %
• Parental protein coverage: 57.55 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  FSSLKDDDSGDHDQNEENSTQKDGEKEKSERDKSQSSSKRKAVVPGPAEHPLQYNYTFWYSRRTPGRPTS
          F..LKDDDSGDHDQNEE.STQKDGEKEKSE..KSQSSSKRKAVVPGPAEH.LQYNYTFWYSRRTPG.PTS
Retrocopy FDALKDDDSGDHDQNEEKSTQKDGEKEKSEQEKSQSSSKRKAVVPGPAEHLLQYNYTFWYSRRTPGWPTS

Parental  SQSYEQNIKQIGTFASVEQFWRFYSHMVRPGDLTGHSDFHLFKEGIKPMWEDDANKNGGKWIIRLRKGLA
          SQSY.QNIKQIGTF.SVE.FWRFYSHMVR..DLTGHSDFHLFKEGIKPM.EDDANKNG.KWIIRL.KGLA
Retrocopy SQSYKQNIKQIGTFTSVEPFWRFYSHMVRLRDLTGHSDFHLFKEGIKPMGEDDANKNGSKWIIRLCKGLA

Parental  S
          S
Retrocopy S

Legend:

• *: Stop codon
• >: Forward frameshift by one nucleotide
• <: Reverse frameshift by one nucleotide

Expression

RNA-Seq

Sarcophilus harrisii was not studied using RNA-Seq expression data.

ChIP-Seq

Sarcophilus harrisii was not studied using ChIP-Seq data.

EST

Sarcophilus harrisii was not studied using EST data.

TSS

Sarcophilus harrisii was not studied using FANTOM5 data.

Lab

retro_shar_101 was not experimentally validated.

Homology

Retrocopy orthology:

Sarcophilus harrisii 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 19 parental genes, and 39 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000016456	1 retrocopy	retro_amel_1304,
Bos taurus	ENSBTAG00000010598	2 retrocopies	retro_btau_1232, retro_btau_1498,
Canis familiaris	ENSCAFG00000011328	1 retrocopy	retro_cfam_183,
Choloepus hoffmanni	ENSCHOG00000013109	3 retrocopies	retro_chof_1963, retro_chof_369, retro_chof_567,
Callithrix jacchus	ENSCJAG00000013786	2 retrocopies	retro_cjac_1061, retro_cjac_2717,
Dasypus novemcinctus	ENSDNOG00000016877	1 retrocopy	retro_dnov_1374,
Equus caballus	ENSECAG00000020187	2 retrocopies	retro_ecab_300, retro_ecab_847,
Erinaceus europaeus	ENSEEUG00000015153	2 retrocopies	retro_eeur_57, retro_eeur_668,
Echinops telfairi	ENSETEG00000007930	1 retrocopy	retro_etel_1385,
Homo sapiens	ENSG00000135930	1 retrocopy	retro_hsap_2689,
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,
Nomascus leucogenys	ENSNLEG00000014333	1 retrocopy	retro_nleu_1189,
Otolemur garnettii	ENSOGAG00000009155	1 retrocopy	retro_ogar_104,
Pan troglodytes	ENSPTRG00000013043	1 retrocopy	retro_ptro_1816,
Sarcophilus harrisii	ENSSHAG00000013108	1 retrocopy	retro_shar_101 ,
Ictidomys tridecemlineatus	ENSSTOG00000003508	3 retrocopies	retro_itri_1270, retro_itri_1370, retro_itri_573,
Tupaia belangeri	ENSTBEG00000004455	11 retrocopies	retro_tbel_1299, retro_tbel_2197, retro_tbel_2623, retro_tbel_2680, retro_tbel_3932, retro_tbel_4471, retro_tbel_4622, retro_tbel_536, retro_tbel_616, retro_tbel_650, retro_tbel_714,