RetrogeneDB ID: retro_itri_1122

Retrocopy location

• Organism: Squirrel (Ictidomys tridecemlineatus)
• Coordinates: JH393381.1:2436845..2437365(+)
• Located in intron of: ENSSTOG00000006287

Retrocopy information

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

Parental gene information

• Parental gene symbol: MRPL32
• Ensembl ID: ENSSTOG00000013340
• Aliases: None
• Description: mitochondrial ribosomal protein L32 [Source:HGNC Symbol;Acc:14035]

Sequence

>retro_itri_1122
GCATCTGGCGTGCTGTTGACCGTGGTGCCTCGGTAGCCCACAGCATGTGGACTGCTCTAAAACTCTTGAGAGCTACTGTA
GCAAAAATGTCAACAGAGCTGGCCAGGGTTTCCAGGCCCTCCCTGGGGGCCAGCATTAGCAGTCCTGGGTCCAGCCATAT
TTAAAGCACAGGCAAATGATACCAGTGGAAGTAAGGAGAATTCCAGCCTTTTGGATGACATCTTTTGGATGGCAGCTCCT
CCAAACAGACACAGCATTGAAGTTAAACAGCATAGGAGAAGAAACCCTCAGAAACTTTATTAAATGTGAGAATATAGACA
TTTGTTCTGAACATGGACATCTGAAACAGAAGCATGTCCTTTGTGGCTATTACAATGAGAAGGTGAGCAAGGAGACCACA
GAAATCAGACAGCAGTTAGGGAAACAAGAAGGGGGTCCTTTTAAGGCTTCTACAGTAGGAGCTGTCATGCTGTACAAAGG
AGAGACACTACATGAACACAATCAGGGCAAGAGGATCATC

Alignment

ORF - retro_itri_1122 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 69.71 %
• Parental protein coverage: 92.43 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  ASGMLLVVVPPWPAARGLLRNCWELLQRKLQKSWPGYPAPPWGPALAVQGPAIF---TNDSCGSKENSNF
          ASG.LL.VVP..P.A.GLL.N..ELL..K.Q.SWPG.P.PPWGPALAV.GPAIF....ND..GSKENS..
Retrocopy ASGVLLTVVPR*PTACGLL*NS*ELL*QKCQQSWPGFPGPPWGPALAVLGPAIFKAQANDTSGSKENSSL

Parental  LDNIFWMAAPKNRRSIEVNRCRRRNPHKL-IKVKNNIDICPECGHLKQKHVLCGYCYEKVCKEAREIRQQ
          LD.IFWMAAP.NR.SIEV...RRRNP.KL.IK..N.IDIC.E.GHLKQKHVLCGY..EKV.KE..EIRQQ
Retrocopy LDDIFWMAAPPNRHSIEVKQHRRRNPQKL>IKCEN-IDICSEHGHLKQKHVLCGYYNEKVSKETTEIRQQ

Parental  IRKQEGGPFKAPTVETVVLYSGETPSENDQGKRII
          ..KQEGGPFKA.TV..V.LY.GET..E..QGKRII
Retrocopy LGKQEGGPFKASTVGAVMLYKGETLHEHNQGKRII

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_1122 retrocopy.

TSS

Ictidomys tridecemlineatus was not studied using FANTOM5 data.

Lab

retro_itri_1122 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 7 parental genes, and 8 retrocopies.

Species	Parental gene accession	Retrocopies number
Mustela putorius furo	ENSMPUG00000018146	1 retrocopy	retro_mputfur_60,
Mus musculus	ENSMUSG00000015672	1 retrocopy	retro_mmus_61,
Oryctolagus cuniculus	ENSOCUG00000012098	1 retrocopy	retro_ocun_474,
Otolemur garnettii	ENSOGAG00000016806	2 retrocopies	retro_ogar_1965, retro_ogar_2797,
Rattus norvegicus	ENSRNOG00000015989	1 retrocopy	retro_rnor_460,
Ictidomys tridecemlineatus	ENSSTOG00000013340	1 retrocopy	retro_itri_1122 ,
Tarsius syrichta	ENSTSYG00000014296	1 retrocopy	retro_tsyr_1710,