RetrogeneDB ID: retro_itri_347

Retrocopy location

• Organism: Squirrel (Ictidomys tridecemlineatus)
• Coordinates: JH393285.1:431327..432414(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSSTOG00000004003
• Aliases: None
• Description: None

Sequence

>retro_itri_347
AGCCCAGGGAGTGGAAAATATGATTTCTTTATTGGTTTGGGATTGGCTGTGACCTCCAGCATTTTCATAGGAGGGAGTTT
CATTTTGAAAAAAAAAAAAAAAAAAGGCCTTCTGCGACTTGCCAGAAAAGGATCCATGAGAGCAGGTCAAGGTGGCCATG
CATATCTTAAAGAATGGTTGTGGTGGGCTGGACTACTGTCAATGGGGGGAATGGGGGCAGGCCAGGAGGCCAACTTCGCT
GCATATGCCTTTGCACCAGCCACGCTAGTGACTCCACTGGGAGTTCTCAGCGTCCTCGTAAGTGCCGTTCTTTCTGCATA
CTTTCTAAATGAAAGACTTAATCTTCATGGGAAAATTGGATGTTTGCTAAACATTCTAGGATCTACAGTCATGGTCATCC
ATGCTCCAAAGGAAGAGGAGATTGAGATGTGAAATGAAATGTCACACAAGTTAGGTGATCCAGGTTTTGTGGTATTTGCA
ACAATTGTGGTCATTGTGTCCTTGATATTAATCTTTGTGGTGGGACCTCGCAAAGGACAGACAAATATTCTTGTGTACAT
AACAGTCTGCTCTGTGATTGGAGCGTTTTTCAGTGTCCTGTGCAAAGGGTTTGGGCATCACCATCAAAGAACTGTTAGCT
GGAAAGCCTGCACTGCGGCACCCCCTGGCCTGGATTCTGCTGCTGAGCCTGGTCATCTGTGTGAGCACACAGATCAATTA
CCTAAACCCTGCCCTAGTCATATTCAACGCTTCCCTTGTAAAACCAATATATTACGTTTTCTTAGTTTTAACTTGTTCAG
CTATTCTTTTTAAGGAGTGGCACGATATGCCTGCTGATGATATCATTGGGACTCTGAGTGGCTTCTTCACAATCATTGTG
GGGGTATTCTTGTTGCATGCCTTTAAAGATGTCAGCTTTAGTTTAGCAAGTCTGCCTGTGTCTTTTCGAAAAGATGATAA
AACAATGAATGGCAATCTCCCTACTATGTATGAAGTTCTTAATAATAATGAAGAAAGCTTATCCTGTGGAATTGAACAAC
ACACTGGTGAGAATATCTCATGGAGAAATGGAAATCTGACAGGTTTT

Alignment

ORF - retro_itri_347 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 89.89 %
• Parental protein coverage: 99.72 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  SPGRGKYDFYIGLGLAMTSSIFIGGSFILKKK---GLLRLARKGSMRAGQGGHAYLKEWLWWAGLLS---
          SPG.GKYDF.IGLGLA.TSSIFIGGSFIL......GLLRLARKGSMRAGQGGHAYLKEWLWWAGLLS...
Retrocopy SPGSGKYDFFIGLGLAVTSSIFIGGSFILXXXXXXGLLRLARKGSMRAGQGGHAYLKEWLWWAGLLSMGG

Parental  MGAGEVANFAAYAFAPATLVTPLGALSVLVSAILSSYFLNERLNLHGKIGCLLSILGSTVMVIHAPKEEE
          MGAG..ANFAAYAFAPATLVTPLG.LSVLVSA.LS.YFLNERLNLHGKIGCLL.ILGSTVMVIHAPKEEE
Retrocopy MGAGQEANFAAYAFAPATLVTPLGVLSVLVSAVLSAYFLNERLNLHGKIGCLLNILGSTVMVIHAPKEEE

Parental  IETLNEMSHKLGDPGFVVFATIVVIVSLILIFVVGPRHGQTNILVYITICSVIGA-FSVSCAKGLGITIK
          IE..NEMSHKLGDPGFVVFATIVVIVSLILIFVVGPR.GQTNILVYIT.CSVIGA.FSVSCAKGLGITIK
Retrocopy IEM*NEMSHKLGDPGFVVFATIVVIVSLILIFVVGPRKGQTNILVYITVCSVIGA>FSVSCAKGLGITIK

Parental  ELLAGKPVLRHPLAWILLLSLVICVSTQINYLNRALDIFNTSLVTPIYYVFFTTSVLTCSAILFKEWQDM
          ELLAGKP.LRHPLAWILLLSLVICVSTQINYLN.AL.IFN.SLV.PIYYVF....VLTCSAILFKEW.DM
Retrocopy ELLAGKPALRHPLAWILLLSLVICVSTQINYLNPALVIFNASLVKPIYYVFL---VLTCSAILFKEWHDM

Parental  PADDIIGTLSGFFTIIVGIFLLHAFKDVSFSLASLPVSFRKDDKAMNGNLPTMYEVLNNNEESLTCGIEQ
          PADDIIGTLSGFFTIIVG.FLLHAFKDVSFSLASLPVSFRKDDK.MNGNLPTMYEVLNNNEESL.CGIEQ
Retrocopy PADDIIGTLSGFFTIIVGVFLLHAFKDVSFSLASLPVSFRKDDKTMNGNLPTMYEVLNNNEESLSCGIEQ

Parental  HTGENISRRNGNLTGF
          HTGENIS.RNGNLTGF
Retrocopy HTGENISWRNGNLTGF

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_347 retrocopy.

TSS

Ictidomys tridecemlineatus was not studied using FANTOM5 data.

Lab

retro_itri_347 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 10 parental genes, and 14 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000013824	1 retrocopy	retro_amel_1163,
Choloepus hoffmanni	ENSCHOG00000005553	1 retrocopy	retro_chof_9,
Callithrix jacchus	ENSCJAG00000005448	1 retrocopy	retro_cjac_1506,
Equus caballus	ENSECAG00000006379	1 retrocopy	retro_ecab_656,
Felis catus	ENSFCAG00000023073	1 retrocopy	retro_fcat_246,
Macaca mulatta	ENSMMUG00000003892	1 retrocopy	retro_mmul_1510,
Mus musculus	ENSMUSG00000030452	1 retrocopy	retro_mmus_3551,
Oryctolagus cuniculus	ENSOCUG00000010746	3 retrocopies	retro_ocun_1581, retro_ocun_773, retro_ocun_809,
Ictidomys tridecemlineatus	ENSSTOG00000004003	3 retrocopies	retro_itri_1847, retro_itri_347 , retro_itri_388,
Vicugna pacos	ENSVPAG00000000671	1 retrocopy	retro_vpac_285,