RetrogeneDB ID: retro_itri_180

Retrocopy location

• Organism: Squirrel (Ictidomys tridecemlineatus)
• Coordinates: AGTP01147661.1:58..531(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: COMMD2
• Ensembl ID: ENSSTOG00000010888
• Aliases: None
• Description: COMM domain containing 2 [Source:HGNC Symbol;Acc:24993]

Sequence

>retro_itri_180
AATGTCTATGAGGGTGCCACCAGGAAGCTCAACCTGAGCAGCAACACGGTCCAGCATGGTGTGGAAGGGTTGACCTACCT
GCTCACTGAGAGCTCCAAGCTCATGATTTCTGAAGTGGATTTCCAAGACTGTTTTTGTTCTGGGATTCTCTGAAGAACTG
AACAATTTATTGCTTCCACTTTACTTGGACAACAGAAAAGAGATCAGGACTATTCTGGGTGAATTGGCACCCAGCCTTCC
CAGTTACCATAGCCTTGATTGGTGACTAGATTTACAGCTTGCAAGAAGAAGCCTCAGGCAACAGATTAAGCCAGCCATAA
CTTTAAAACTAAACCTAAATCTGAGTGGAGACCACAATACCAAAGTTCTGCAGACAGACTCAGCCACCCTACTTCATTTT
AGTTCAGCAACTGTAACAATCCTTGGAGGAAATAAAAACAAACCACTGTAGGAGAGTAGTTCACAACATCAAG

Alignment

ORF - retro_itri_180 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 80.62 %
• Parental protein coverage: 81.87 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  NKKKNVARKLNVSSDAVQHGVEGLTYLLTESSKLMISEVDFQDSVFVLG-FSEELNKLLLQLYLDNRKEI
          N......RKLN.SS..VQHGVEGLTYLLTESSKLMISEVDFQD..F..G.FSEELN.LLL.LYLDNRKEI
Retrocopy NVYEGATRKLNLSSNTVQHGVEGLTYLLTESSKLMISEVDFQD-CFCSG>FSEELNNLLLPLYLDNRKEI

Parental  RTILGELAPSLPSYHSLEWRLDVQLASRSLRQQIKPAVTIKLHLNQNGDHNTKVLQTDPATLLH-LVQQL
          RTILGELAPSLPSYHSL.W.LD.QLA.RSLRQQIKPA.T.KL.LN..GDHNTKVLQTD.ATLLH.LVQQL
Retrocopy RTILGELAPSLPSYHSLDW*LDLQLARRSLRQQIKPAITLKLNLNLSGDHNTKVLQTDSATLLH>LVQQL

Parental  EQALEEMKTNHCRRVVRNIK
          .Q.LEE.KTNHCRRVV.NIK
Retrocopy *QSLEEIKTNHCRRVVHNIK

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_180 retrocopy.

TSS

Ictidomys tridecemlineatus was not studied using FANTOM5 data.

Lab

retro_itri_180 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 6 parental genes, and 10 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000013809	1 retrocopy	retro_chof_1601,
Cavia porcellus	ENSCPOG00000005273	2 retrocopies	retro_cpor_520, retro_cpor_956,
Rattus norvegicus	ENSRNOG00000043386	1 retrocopy	retro_rnor_2231,
Ictidomys tridecemlineatus	ENSSTOG00000010888	4 retrocopies	retro_itri_180 , retro_itri_1803, retro_itri_1880, retro_itri_1899,
Tupaia belangeri	ENSTBEG00000003545	1 retrocopy	retro_tbel_2895,
Tursiops truncatus	ENSTTRG00000003450	1 retrocopy	retro_ttru_1759,