RetrogeneDB ID: retro_itri_1526

Retrocopy location

• Organism: Squirrel (Ictidomys tridecemlineatus)
• Coordinates: JH393525.1:1739480..1740215(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSSTOG00000000014
• Aliases: None
• Description: None

Sequence

>retro_itri_1526
ATTCCTTTTGGTTCCAAGTCCAAGATGGCAAGTCTCAAGGATCAGCTAATTGTGAACCTTCTTAAGGAAGAACAGGTCCC
CCAGAATAAGATTACAGTTGTTAGAGTTGGTGCTGTTGGCATGGCCTGTGCCATCAGTATCTTAATGAAGGACTTGACAG
ATGAACTTGTTCTTATTTTCATGGAAGATAAATTGAAGGGAGAGATGATGGAGCTCCAGCATGGCAGCCTTTTTCTTAGA
ACACCAAAAATTGTCTCTGCAAAAACTATAATGTGACTGCAAACTCCAAACTCGTTATTATCACAGCTGGGGCACATCAG
CAAGAGGGAGAAAGCTGTCTTAATTTGGTCCAGCGTAATGTGAACATCTTCAAGTTCATCATTCCCAGTGTTGTAAAAAA
AGAGCCCACATTGCAAGTTGATTATTGTTTCCAATACAGTGGATATCTTGACCTATGTGGCTTGGAAGATAAGTGGATTT
CTCAAAAACCGTTTTATTGGAAGTGGTTGCAATCTGGATTCAGCACTGTTTCATTACCTGATGGGGGAAAGGCTGAGAGT
TCACCCATTAAGCTGTCATGGATGGGTCCTTGGGGAGCATGGAGACCTTAGTGTACCTGTGTGGAGTAGAGTGAATGTTT
CTGGTGTCTCCTTGAAGAATCTGCACCCAGATTTGGGCACTGATGCAGATAAGGAACATTGGAAAGAGGTTCATAAGCAG
GTGGTTGACAGCGCG

Alignment

ORF - retro_itri_1526 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 89.92 %
• Parental protein coverage: 68.14 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  IPFGSKSKMASLKDQLIVNLLKEEQVPQNKITVVGVGAVGMACAISILMKDLADELALVDVMEDKLKGEM
          IPFGSKSKMASLKDQLIVNLLKEEQVPQNKITVV.VGAVGMACAISILMKDL.DEL.L...MEDKLKGEM
Retrocopy IPFGSKSKMASLKDQLIVNLLKEEQVPQNKITVVRVGAVGMACAISILMKDLTDELVLI-FMEDKLKGEM

Parental  MDLQHGSLFLRTPKIVSGK-DYNVTANSKLVIITAGARQQEGESRLNLVQRNVNIFKFIIPNVVKY-SPH
          M.LQHGSLFLRTPKIVS.K..YNVTANSKLVIITAGA.QQEGES.LNLVQRNVNIFKFIIP.VVK..SPH
Retrocopy MELQHGSLFLRTPKIVSAK<NYNVTANSKLVIITAGAHQQEGESCLNLVQRNVNIFKFIIPSVVKK>SPH

Parental  CKLLIVSNPVDILTYVAWKISGFPKNRVIGSGCNLDSARFRYLMGERLGVHPLSCHGWVLGEHGDSSVPV
          CKL.IVSN.VDILTYVAWKISGF.KNR.IGSGCNLDSA.F.YLMGERL.VHPLSCHGWVLGEHGD.SVPV
Retrocopy CKLIIVSNTVDILTYVAWKISGFLKNRFIGSGCNLDSALFHYLMGERLRVHPLSCHGWVLGEHGDLSVPV

Parental  WSGVNVAGVSLKNLHPDLGTDADKEHWKEVHKQVVDSA
          WS.VNV.GVSLKNLHPDLGTDADKEHWKEVHKQVVDSA
Retrocopy WSRVNVSGVSLKNLHPDLGTDADKEHWKEVHKQVVDSA

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_1526 retrocopy.

TSS

Ictidomys tridecemlineatus was not studied using FANTOM5 data.

Lab

retro_itri_1526 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 8 parental genes, and 32 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000009211	8 retrocopies	retro_cfam_1061, retro_cfam_1149, retro_cfam_1182, retro_cfam_1317, retro_cfam_1617, retro_cfam_1946, retro_cfam_2006, retro_cfam_309,
Dipodomys ordii	ENSDORG00000003524	2 retrocopies	retro_dord_439, retro_dord_449,
Felis catus	ENSFCAG00000015735	4 retrocopies	retro_fcat_102, retro_fcat_1839, retro_fcat_1919, retro_fcat_295,
Myotis lucifugus	ENSMLUG00000016343	4 retrocopies	retro_mluc_1716, retro_mluc_2031, retro_mluc_2440, retro_mluc_365,
Mustela putorius furo	ENSMPUG00000013730	5 retrocopies	retro_mputfur_1256, retro_mputfur_133, retro_mputfur_1446, retro_mputfur_1476, retro_mputfur_1565,
Ictidomys tridecemlineatus	ENSSTOG00000000014	3 retrocopies	retro_itri_1396, retro_itri_1526 , retro_itri_535,
Ictidomys tridecemlineatus	ENSSTOG00000022058	2 retrocopies	retro_itri_501, retro_itri_648,
Tarsius syrichta	ENSTSYG00000008062	4 retrocopies	retro_tsyr_1811, retro_tsyr_2064, retro_tsyr_2071, retro_tsyr_731,