RetrogeneDB ID: retro_itri_640

Retrocopy location

• Organism: Squirrel (Ictidomys tridecemlineatus)
• Coordinates: JH393308.1:3029785..3030184(-)
• Located in intron of: ENSSTOG00000010701

Retrocopy information

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

Parental gene information

• Parental gene symbol: FABP3
• Ensembl ID: ENSSTOG00000003842
• Aliases: None
• Description: Fatty acid-binding protein, heart [Source:UniProtKB/Swiss-Prot;Acc:Q99P61]

Sequence

>retro_itri_640
ATGGTGGACGCCTTCGTGGGCACCTGGAAACTAGTGGACAGCAAGAATTTCGATGACTACATGAAGTCACTTGATGTGGG
CTTTGCTACCAGGCAAGTGGCCAGCATGACCAAGCCCACTACAATCATTGAAAAGAATGGGGACACCATCATCTTAAAAA
CACAGAGCACCTTCAAGAATTTGGAGATCGGTTTTTAACTGGGGGTAGAGTTTGATGAGACTACAGCAGATGACAGGAAG
GTCAAGTCCACTGTGATGTTGGATGGAGGAAAACTTGTCCATGTGCAGAAGTGGGATGGGCAAGAGACTACACTTGTGCG
GGAGCTAAATAATGGGAAACTCATCTTGACACTCACCCATGGCAGTGTAGTGTGCACTTGCACTTATGAGAAAGAGGCA

Alignment

ORF - retro_itri_640 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 93.98 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MVDAFVGTWKLVDSKNFDDYMKSLGVGFATRQVASMTKPTTIIEKNGDTIILKTQSTFKNTEISFQLGKE
          MVDAFVGTWKLVDSKNFDDYMKSL.VGFATRQVASMTKPTTIIEKNGDTIILKTQSTFKN.EI.F.LG.E
Retrocopy MVDAFVGTWKLVDSKNFDDYMKSLDVGFATRQVASMTKPTTIIEKNGDTIILKTQSTFKNLEIGF*LGVE

Parental  FDETTADDRKVKSTVTLDGGKLVHVQKWDGQETTLVRELNDGKLILTLTHGSVVCTRTYEKEA
          FDETTADDRKVKSTV.LDGGKLVHVQKWDGQETTLVRELN.GKLILTLTHGSVVCT.TYEKEA
Retrocopy FDETTADDRKVKSTVMLDGGKLVHVQKWDGQETTLVRELNNGKLILTLTHGSVVCTCTYEKEA

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_640 retrocopy.

TSS

Ictidomys tridecemlineatus was not studied using FANTOM5 data.

Lab

retro_itri_640 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 18 parental genes, and 38 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000016819	2 retrocopies	retro_btau_1467, retro_btau_295,
Danio rerio	ENSDARG00000023290	1 retrocopy	retro_drer_33,
Dasypus novemcinctus	ENSDNOG00000000511	2 retrocopies	retro_dnov_1510, retro_dnov_2482,
Equus caballus	ENSECAG00000024852	1 retrocopy	retro_ecab_519,
Homo sapiens	ENSG00000121769	1 retrocopy	retro_hsap_1258,
Gorilla gorilla	ENSGGOG00000014432	1 retrocopy	retro_ggor_990,
Macropus eugenii	ENSMEUG00000012501	6 retrocopies	retro_meug_1037, retro_meug_148, retro_meug_1660, retro_meug_273, retro_meug_563, retro_meug_819,
Microcebus murinus	ENSMICG00000009359	4 retrocopies	retro_mmur_1490, retro_mmur_203, retro_mmur_621, retro_mmur_734,
Myotis lucifugus	ENSMLUG00000013609	2 retrocopies	retro_mluc_1144, retro_mluc_1717,
Mus musculus	ENSMUSG00000028773	3 retrocopies	retro_mmus_2804, retro_mmus_3204, retro_mmus_65,
Nomascus leucogenys	ENSNLEG00000001586	1 retrocopy	retro_nleu_2097,
Otolemur garnettii	ENSOGAG00000013757	4 retrocopies	retro_ogar_1148, retro_ogar_1312, retro_ogar_1873, retro_ogar_959,
Pongo abelii	ENSPPYG00000001616	1 retrocopy	retro_pabe_1048,
Pan troglodytes	ENSPTRG00000000457	1 retrocopy	retro_ptro_3047,
Rattus norvegicus	ENSRNOG00000012879	1 retrocopy	retro_rnor_2199,
Ictidomys tridecemlineatus	ENSSTOG00000003842	3 retrocopies	retro_itri_1544, retro_itri_640 , retro_itri_641,
Ictidomys tridecemlineatus	ENSSTOG00000005673	1 retrocopy	retro_itri_749,
Ictidomys tridecemlineatus	ENSSTOG00000007877	3 retrocopies	retro_itri_1305, retro_itri_389, retro_itri_72,