RetrogeneDB ID: retro_itri_1298

Retrocopy location

• Organism: Squirrel (Ictidomys tridecemlineatus)
• Coordinates: JH393431.1:82291..82979(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSSTOG00000016391
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: ANKRD46
• Ensembl ID: ENSSTOG00000024280
• Aliases: None
• Description: ankyrin repeat domain 46 [Source:HGNC Symbol;Acc:27229]

Sequence

>retro_itri_1298
ATGTCCTATGTTTTTGTAAATGATTCTTCTCAAACTAATGTGCCCTTGCTACAAGCCTGTATTGATGGAGACTTTAACTA
TTCTAATAGGCTTCTGGAAAGTGGCTTTGACCCAAATATCCGTGACAGCAGGGGCAGGACAGGCCTTCACCTTGCAGCAG
CCCGAGGGAATGTAGATATCTGCCAGCTGTTGCATAAATTTGGTGCTGACCTTCTAGCCACAGATTACCAAGGAAACACA
GCTCTTCATCTCTGTGGCCATGTGGATACCATCCAATTCTTAGTTTCCAATGGACTCAAAATTGATATATGCAATCATCA
AGGTGCTACTCCTTTAGTTCTGGCAAAGCACAAGGAGAGTGAATAAAGATGTCATCCGATTGCTGGAATCTTTGGAAGAA
CAGGAGGTAAAAGGATTTAACAGAGGAACCCACTCAAAACTGGAGACCATGCAGACAGCTGAGAGTGAAAGTGCCATGGA
AAGCCATTCTCTCCTCAATCCCAACCTACAGCAGCAAGGTGAAGGAGTCCTTTCCAGCTTTCGAACCACATGGCAGGAGT
TCGTAGAGGATCTGGGCTTCTGGAGGGTCCTGCTCCTGATCTTTGTCATTGCTTTACTGTCTCTTGGCATTGCCTACTAC
GTGAGCGGAGTGCTGCCCTTTGTGGAAAACCAGCCTGAACTGGTGCAT

Alignment

ORF - retro_itri_1298 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 97.83 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MSYVFVNDSSQTNVPLLQACIDGDFNYSKRLLESGFDPNIRDSRGRTGLHLAAARGNVDICQLLHKFGAD
          MSYVFVNDSSQTNVPLLQACIDGDFNYS.RLLESGFDPNIRDSRGRTGLHLAAARGNVDICQLLHKFGAD
Retrocopy MSYVFVNDSSQTNVPLLQACIDGDFNYSNRLLESGFDPNIRDSRGRTGLHLAAARGNVDICQLLHKFGAD

Parental  LLATDYQGNTALHLCGHVDTIQFLVSNGLKIDICNHQGATPLVLAKR-RGVNKDVIRLLESLEEQEVKGF
          LLATDYQGNTALHLCGHVDTIQFLVSNGLKIDICNHQGATPLVLAK..R.VNKDVIRLLESLEEQEVKGF
Retrocopy LLATDYQGNTALHLCGHVDTIQFLVSNGLKIDICNHQGATPLVLAKH>RRVNKDVIRLLESLEEQEVKGF

Parental  NRGTHSKLETMQTAESESAMESHSLLNPNL-QQGEGVLSSFRTTWQEFVEDLGFWRVLLLIFVIALLSLG
          NRGTHSKLETMQTAESESAMESHSLLNPNL.QQGEGVLSSFRTTWQEFVEDLGFWRVLLLIFVIALLSLG
Retrocopy NRGTHSKLETMQTAESESAMESHSLLNPNLQQQGEGVLSSFRTTWQEFVEDLGFWRVLLLIFVIALLSLG

Parental  IAYYVSGVLPFVENQPELVH
          IAYYVSGVLPFVENQPELVH
Retrocopy IAYYVSGVLPFVENQPELVH

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_1298 retrocopy.

TSS

Ictidomys tridecemlineatus was not studied using FANTOM5 data.

Lab

retro_itri_1298 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 2 parental genes, and 3 retrocopies.

Species	Parental gene accession	Retrocopies number
Ictidomys tridecemlineatus	ENSSTOG00000024280	2 retrocopies	retro_itri_1298 , retro_itri_293,
Tupaia belangeri	ENSTBEG00000011202	1 retrocopy	retro_tbel_4097,