RetrogeneDB ID: retro_itri_1324

Retrocopy location

• Organism: Squirrel (Ictidomys tridecemlineatus)
• Coordinates: JH393440.1:4248393..4248719(-)
• Located in intron of: ENSSTOG00000014235

Retrocopy information

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

Parental gene information

• Parental gene symbol: KIAA0101
• Ensembl ID: ENSSTOG00000019643
• Aliases: None
• Description: KIAA0101 [Source:HGNC Symbol;Acc:28961]

Sequence

>retro_itri_1324
ATGGTGTGGACTAAAGCAGACAGTGTCCCAGGCACCTACAGATAAGTGGTAGCTTCTCAAGCTCCAAGAAATGTCCTTGG
TTCCTTCACCTCTGCCACTAATTCTACATTGCTTTTATCAAGGAAAGCTGAAAATGCAGGAAGGAATCTAGTTTGTATAT
GTCCAACTCCCCAGTGGCAAAAAGGAAATGGAAAATTCTTCAGGCTGCCCCTAAAGATTCTGAAAAGGAGAATCAGATTA
CTGAAGAGGTAGGCAGCAGTGGTTTAGGAAAAGCAAAGAAGACAGTATGACCTTTGCAACTTCACCACAGAGATGATGAA
AAAGAA

Alignment

ORF - retro_itri_1324 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 72.32 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 2
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MVRTKADSVPGTYRKVVASRAPRKILGSSSSATNSASLSSRKAENKYAGGNPVCVRPTPKWQKGIGEFFR
          MV.TKADSVPGTYR.VVAS.APR..LGS..SATNS..L.SRKAEN..AG.N.VC..PTP.WQKG.G.FFR
Retrocopy MVWTKADSVPGTYR*VVASQAPRNVLGSFTSATNSTLLLSRKAEN--AGRNLVCICPTPQWQKGNGKFFR

Parental  L-SPKDSEKENRIPEEPGSSGLGKAKRKACPLQPDHTDDEKE
          L..PKDSEKEN.I.EE.GSSGLGKAK....PLQ..H.DDEKE
Retrocopy L<APKDSEKENQITEEVGSSGLGKAKKTV*PLQLHHRDDEKE

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_1324 retrocopy.

TSS

Ictidomys tridecemlineatus was not studied using FANTOM5 data.

Lab

retro_itri_1324 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 9 parental genes, and 27 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000010763	2 retrocopies	retro_chof_1104, retro_chof_892,
Cavia porcellus	ENSCPOG00000006482	3 retrocopies	retro_cpor_138, retro_cpor_186, retro_cpor_365,
Dipodomys ordii	ENSDORG00000014912	1 retrocopy	retro_dord_674,
Monodelphis domestica	ENSMODG00000027710	2 retrocopies	retro_mdom_1275, retro_mdom_776,
Mus musculus	ENSMUSG00000040204	7 retrocopies	retro_mmus_1088, retro_mmus_1289, retro_mmus_1335, retro_mmus_1844, retro_mmus_2809, retro_mmus_2964, retro_mmus_378,
Otolemur garnettii	ENSOGAG00000003982	1 retrocopy	retro_ogar_501,
Rattus norvegicus	ENSRNOG00000016561	5 retrocopies	retro_rnor_1162, retro_rnor_1412, retro_rnor_2595, retro_rnor_2624, retro_rnor_2698,
Ictidomys tridecemlineatus	ENSSTOG00000019643	4 retrocopies	retro_itri_1241, retro_itri_1324 , retro_itri_1888, retro_itri_929,
Tupaia belangeri	ENSTBEG00000013732	2 retrocopies	retro_tbel_3099, retro_tbel_4093,