RetrogeneDB ID: retro_itri_583

Retrocopy location

• Organism: Squirrel (Ictidomys tridecemlineatus)
• Coordinates: JH393303.1:12494781..12495231(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: FAM206A
• Ensembl ID: ENSSTOG00000027231
• Aliases: None
• Description: family with sequence similarity 206, member A [Source:HGNC Symbol;Acc:1364]

Sequence

>retro_itri_583
CTCATGAATTCTAACTTTACTCAGTGGTATAAAGCAGATGTCAAAGGAAAAACCCTGTGAGTATCACTTTATACAACAGT
ACTCAAGCTGGAATATGTGTCATCACATTGACTGGACCTCATTCAGTCCTTCAAAGTAGAAAACCAATTACAAGAATTTG
TTATCAGATGGGTACCAACTATAGCAGACTTCAGAACAAGATTTCTGGGAAATTTAAGTGGAGGAACAGTTTCTAACAGA
ACTTGCACCTCTGTGTAAGATTTACCTCTCAATGGAGAGAAATATGCTTTATCTAGCTATTTTAGAGTACAACTGATGGA
AGCAAATAAAAACATTCTCCACAAGCCATCTATTCTTGAAGAAAAGCTATCCACTGAAGGCTACATTGCAGTTGTGGTAC
CCAAATTTGAAGAAAGCAAAAGGATAATGGATGGGTTACTGACAAAAAGA

Alignment

ORF - retro_itri_583 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 66.23 %
• Parental protein coverage: 82.87 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  LVDRYFTRWYKADVKGK-PCEDHCILQHSN-RICVITLAESHPVLQSGKTIKSISYQISTNCSRLQNKVS
          L....FT.WYKADVKGK.PCE.H.I.Q.S...ICVITL...H.VLQS.K.I..I.YQ..TN.SRLQNK.S
Retrocopy LMNSNFTQWYKADVKGK>PCEYHFIQQYSS>GICVITLTGPHSVLQSRKPITRICYQMGTNYSRLQNKIS

Parental  GKFKRGAQF-LTELAPLCKIYCS-DGEEYTISSCVRGRLMEVNENILHKPSILQEKPSTEGYIAVVLPKF
          GKFK....F.LTELAPLCKIY.S..GE.Y..SS..R..LME.N.NILHKPSIL.EK.STEGYIAVV.PKF
Retrocopy GKFKWRNSF<LTELAPLCKIYLS<NGEKYALSSYFRVQLMEANKNILHKPSILEEKLSTEGYIAVVVPKF

Parental  EESKSVTEGLLTQK
          EESK....GLLT..
Retrocopy EESKRIMDGLLTKR

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_583 retrocopy.

TSS

Ictidomys tridecemlineatus was not studied using FANTOM5 data.

Lab

retro_itri_583 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 13 parental genes, and 13 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000004996	1 retrocopy	retro_btau_873,
Canis familiaris	ENSCAFG00000028510	1 retrocopy	retro_cfam_1345,
Cavia porcellus	ENSCPOG00000005927	1 retrocopy	retro_cpor_1488,
Dipodomys ordii	ENSDORG00000008618	1 retrocopy	retro_dord_611,
Homo sapiens	ENSG00000119328	1 retrocopy	retro_hsap_1197,
Macropus eugenii	ENSMEUG00000013637	1 retrocopy	retro_meug_1321,
Microcebus murinus	ENSMICG00000002074	1 retrocopy	retro_mmur_1363,
Monodelphis domestica	ENSMODG00000012563	1 retrocopy	retro_mdom_1837,
Oryctolagus cuniculus	ENSOCUG00000001882	1 retrocopy	retro_ocun_1527,
Otolemur garnettii	ENSOGAG00000024317	1 retrocopy	retro_ogar_1200,
Pongo abelii	ENSPPYG00000019483	1 retrocopy	retro_pabe_997,
Sorex araneus	ENSSARG00000009305	1 retrocopy	retro_sara_313,
Ictidomys tridecemlineatus	ENSSTOG00000027231	1 retrocopy	retro_itri_583 ,