RetrogeneDB ID: retro_itri_1575

Retrocopy location

• Organism: Squirrel (Ictidomys tridecemlineatus)
• Coordinates: JH393551.1:144886..145791(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSSTOG00000000304
• Aliases: None
• Description: None

Sequence

>retro_itri_1575
ATGGCAGCCCCAGTGCCTTGGAGGTTGTCTTGCTTCTCCAAAGCTTTGGGATGGTGGTCTCGGCAGTCAGTCCTGGGGAC
TCAGTCTAGAGCTGAAGTTCCAGTAAGAACTAAAAAACGTTTGACACCACTTGCTTATGAACCCAAATGCAAAACAGAAA
AGGAGTTTATAGAACATGCCTGGAAAGCAGGATTCCCCTAGAATGTTTCGAATGTCCCAGGCACGTATGTGGCCTGTGCA
GCTGGTATCTTTGATGCTTATGTTCCTCCTGAGGGAAATGCTCAAATGTCATTTCTTTCAAAGGAAGGACTGAAACAGAC
AACTGAGCGTTTGAATAAAAATGCAGACTCACAGTTGTCAATCCAGAACATAAAAGAAATTGATGCTAATTTTTAAACAA
AGAACTTCCCTGAAAAAGCTAAGGATATTTTCATAGAAGCTCACCTTTGTCTAAGCAACTCACACCATGACTGGCTTCAA
GCCTTGGTAACTGAACACTGTTTTCTGGATGTGGTCTGTAATATCAAGTATAAGACTGTCTGCTGGGGCTTTGTGGAATC
TTTAGAGCCGGCCCAGGTGCTTCAGGTTCACTGCTCAAGTAATGGTGAACCAAAGCAACATGTGTGGCCAGGTTACTGTA
CGCACACACAAGGCCATCTATGATTGCATTAGGCAGTTGATATATGGAAAAGAAGGTGTGCTCAAGGTTGTCTTGGAGAA
TGCTGTGTTTGAAAAACACCTGGTGAACTCCTGTGGGAGCTGGAGAATGCATGACAAGATTGGCCCCTCCATGGGTGCCC
CCTATGCAGCCCATCCTTAAAATGGTGATGATTCCTGGCCCCCAGTTGGAACCATGGGGAAAATGTGAAGAGGCACAAAA
AGAGGCCCATATGTCTCAGCTAGCC

Alignment

ORF - retro_itri_1575 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 64.72 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 2
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  MAAPVPRRLASLSKALGWWSRQSLLITQSTAVVPVRTKKRFTPPAYEPKYKTEKEFIEYARKAGLVIPPE
          MAAPVP.RL...SKALGWWSRQS.L.TQS.A.VPVRTKKR.TP.AYEPK.KTEKEFIE.A.KAG...P..
Retrocopy MAAPVPWRLSCFSKALGWWSRQSVLGTQSRAEVPVRTKKRLTPLAYEPKCKTEKEFIEHAWKAG--FP*N

Parental  RLDRPIHVAVLSTSILSVFIPSLKTLSISFFFKERVREERERERENFLTSLLIRKIKEFDANFKTKDFPE
          ....P.........I.....P.......SF..KE......ER...N....L.I..IKE.DANF.TK.FPE
Retrocopy VSNVPGTYVACAAGIFDAYVPPEGNAQMSFLSKEGLKQTTERLNKNADSQLSIQNIKEIDANF*TKNFPE

Parental  KAKDIFIEAHLCLNNSDHDRLHTLVTEHCFPNMVWDIKYKTVRWSFVESLEPAQVVQVRCSS-MVNQSNM
          KAKDIFIEAHLCL.NS.HD.L..LVTEHCF...V..IKYKTV.W.FVESLEPAQV.QV.CSS.MVNQSNM
Retrocopy KAKDIFIEAHLCLSNSHHDWLQALVTEHCFLDVVCNIKYKTVCWGFVESLEPAQVLQVHCSS>MVNQSNM

Parental  YGQVTVRMHTRQTLAIYDRFGRLMYGQEDVPKDVLEYIVFEKHLLNPYGSWRMHGKI-VPPWAPPKQPIL
          .GQVTVR.H.....AIYD....L.YG.E.V.K.VLE..VFEKHL.N..GSWRMH.KI..PPW.PP.QPIL
Retrocopy CGQVTVRTHK----AIYDCIRQLIYGKEGVLKVVLENAVFEKHLVNSCGSWRMHDKI>APPWVPPMQPIL

Parental  KTVMIPGPQLEPWGKCEEAQRENHKSQLA
          K.VMIPGPQLEPWGKCEEAQ.E.H.SQLA
Retrocopy KMVMIPGPQLEPWGKCEEAQKEAHMSQLA

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_1575 retrocopy.

TSS

Ictidomys tridecemlineatus was not studied using FANTOM5 data.

Lab

retro_itri_1575 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 10 retrocopies.

Species	Parental gene accession	Retrocopies number
Felis catus	ENSFCAG00000005808	2 retrocopies	retro_fcat_1677, retro_fcat_283,
Monodelphis domestica	ENSMODG00000012560	1 retrocopy	retro_mdom_403,
Nomascus leucogenys	ENSNLEG00000000530	1 retrocopy	retro_nleu_1967,
Otolemur garnettii	ENSOGAG00000015816	1 retrocopy	retro_ogar_1029,
Pan troglodytes	ENSPTRG00000009065	1 retrocopy	retro_ptro_107,
Ictidomys tridecemlineatus	ENSSTOG00000000304	2 retrocopies	retro_itri_102, retro_itri_1575 ,
Tupaia belangeri	ENSTBEG00000000585	1 retrocopy	retro_tbel_4621,
Vicugna pacos	ENSVPAG00000004977	1 retrocopy	retro_vpac_512,