RetrogeneDB ID: retro_itri_986

Retrocopy location

• Organism: Squirrel (Ictidomys tridecemlineatus)
• Coordinates: JH393355.1:4315042..4315642(-)
• Located in intron of: ENSSTOG00000007094

Retrocopy information

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

Parental gene information

• Parental gene symbol: OCIAD1
• Ensembl ID: ENSSTOG00000014963
• Aliases: None
• Description: OCIA domain containing 1 [Source:HGNC Symbol;Acc:16074]

Sequence

>retro_itri_986
AGATGCTGTGCCTTGGCTGCAACAAGTATGTTGATTACTCAAGGATTGATTAGTAAAGGAATCCTTTCAAGTCATCCCAA
ATATGGTTCCATCCCTAAACTTATATTTGCTTGCATCATGACATACTCTGGTGGAAAGCTCTCGTTCATGGAAACTTGCC
AAGAGAAGTTCAAGAACCTTGAAATTTCCCCCTCTGGGAGAAGATTTACGATCGGAGCAAACACAACGATCTTTGCCACC
TGGGCATTATTCTCAAAAGTCAAAATATGACTCAAATATGAGTGGTCAGTCCTCTTTTGTGACATCCCTAGCAGCAGACA
ACATAGAAAAAGAGATGCTGCCTCATTATGAGTCAATTCCGTGCAGTGCTTCTATGAATGAATCCACTCCCACTGGTATT
ACTGATTATATTGCTCTAGGACCTGATCTCAACCTTGAAGAAAATCCCCAAAGAAAAAAAAATATTACATATGAGGAATT
AGGGAATAAAAATAGAGAGTCATATGAAGTAACTTTAATGCAAAAGACTGCCCCTCAGTCAGGCCTATGCAAGAAAGAGT
GCCAAAAAAAGAAGTCAAAGTAAACAAATATGGAGATACT

Alignment

ORF - retro_itri_986 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 82.18 %
• Parental protein coverage: 80.57 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  RSVPLAATSMLITQGLISKGILSSHPKYGSIPKLIFACIMGYFAGKLSYVKTCQEKFKNLENSP-LGEAL
          R...LAATSMLITQGLISKGILSSHPKYGSIPKLIFACIM.Y..GKLS...TCQEKFKNLE.SP.LGE.L
Retrocopy RCCALAATSMLITQGLISKGILSSHPKYGSIPKLIFACIMTYSGGKLSFMETCQEKFKNLEISP>LGEDL

Parental  RSGQARRSLPPGHYSQKSKYDSNVSDQSSFVTSPAADNIEKEMQPRYEPIPFSASMNESTPTGITDHIAQ
          RS.Q..RSLPPGHYSQKSKYDSN.S.QSSFVTS.AADNIEKEM.P.YE.IP.SASMNESTPTGITD.IA.
Retrocopy RSEQTQRSLPPGHYSQKSKYDSNMSGQSSFVTSLAADNIEKEMLPHYESIPCSASMNESTPTGITDYIAL

Parental  GPDPYLEESPK-RKNITYEELRNKNRESYEVTLTQKTD-PSVRPMQERVPKKEVKVNKYGDT
          GPD..LEE.P.....ITYEEL.NKNRESYEVTL.QKT..PSVRPMQERVPKKEVKVNKYGDT
Retrocopy GPDLNLEENPQXXXXITYEELGNKNRESYEVTLMQKTA<PSVRPMQERVPKKEVKVNKYGDT

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_986 retrocopy.

TSS

Ictidomys tridecemlineatus was not studied using FANTOM5 data.

Lab

retro_itri_986 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 7 parental genes, and 8 retrocopies.

Species	Parental gene accession	Retrocopies number
Cavia porcellus	ENSCPOG00000011863	1 retrocopy	retro_cpor_928,
Echinops telfairi	ENSETEG00000005961	1 retrocopy	retro_etel_1731,
Latimeria chalumnae	ENSLACG00000014002	1 retrocopy	retro_lcha_88,
Macropus eugenii	ENSMEUG00000010655	2 retrocopies	retro_meug_1692, retro_meug_2016,
Monodelphis domestica	ENSMODG00000020640	1 retrocopy	retro_mdom_1103,
Sarcophilus harrisii	ENSSHAG00000018132	1 retrocopy	retro_shar_74,
Ictidomys tridecemlineatus	ENSSTOG00000014963	1 retrocopy	retro_itri_986 ,