RetrogeneDB ID: retro_itri_1241

Retrocopy location

• Organism: Squirrel (Ictidomys tridecemlineatus)
• Coordinates: JH393410.1:4339299..4339625(+)
• Located in intron of: ENSSTOG00000022481

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_1241
AAACTCAAAGCAGACAGTATCCCAAGCACCTACAGAAAAGTGGTGGTTTCTCAAGCCCCAAGAAAGGTCCTTGGTCCCTC
CACCTCAGCCACTAATTATACATGGCTTTCATCAAGGTATGTTGAAAATAAGTATGCAGGAGGAAATCCAGTTTGTGATG
TCCAACCCCCAAGCGGCTAAAAAGGAATTGGAGAATTCTTCAGGCTGTCCCCTAAAGATTTTGAAAAGGAGAATCAGATT
CCTGAAGAGGCAGGAAGCAGTAGCTTAGGAAAAGCAAAGGGAAAAAAGTATGTCCTTTGCAACCTGATCATACAGATGAT
GAAAAA

Alignment

ORF - retro_itri_1241 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 72.73 %
• Parental protein coverage: 97.3 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  RTKADSVPGTYRKVVASRAPRKILGSSSSATNSASLSSRKAENKYAGGNPVCVRPTPKWQKGIGEFFRLS
          ..KADS.P.TYRKVV.S.APRK.LG.S.SATN...LSSR..ENKYAGGNPVC....P...KGIGEFFRLS
Retrocopy KLKADSIPSTYRKVVVSQAPRKVLGPSTSATNYTWLSSRYVENKYAGGNPVCDVQPPSG*KGIGEFFRLS

Parental  PKDSEKENRIPEEPGSSGLG-KAK-RKACPLQPDHTDDEK
          PKD.EKEN.IPEE.GSS.LG.K.K..K.CPLQPDHTDDEK
Retrocopy PKDFEKENQIPEEAGSSSLG<KSKGKKVCPLQPDHTDDEK

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_1241 retrocopy.

TSS

Ictidomys tridecemlineatus was not studied using FANTOM5 data.

Lab

retro_itri_1241 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,