RetrogeneDB ID: retro_sara_223

Retrocopy location

• Organism: Shrew (Sorex araneus)
• Coordinates: scaffold_101447:2..693(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSSARG00000006253
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: PIM2
• Ensembl ID: ENSSARG00000008832
• Aliases: None
• Description: pim-2 oncogene [Source:HGNC Symbol;Acc:8987]

Sequence

>retro_sara_223
ATCAAAGTGATCTCCCGGAACCGTGTGCTGGACTGGTCCCCCTTGCCTGATTCTGGCACATGCCCACTGGAAGTGGCCCT
GCTGTGGAAAGTGGGTGCCGGCGGTGGACATCCTGGTGTGATCCGCCTCCTCGACTGGTTTGAGACAGCTGAGGGCTTCA
TGCTGGTCCTTGAGCGCCCTTTGCCAGCCCAGGATCTCTTTGACTACATCACAGAGCAGGGTCCACTGGGTGAAAACCGA
AGCCGCAGCCTCTTTGCCCAAGTAGTGGCAGCGGTTCAGCACTGCCATGCCCGTGGTGTTGTCCACCGTGACATCAAGGA
TGAAAACATCTTGATGGACCTCCGCCGGGGCTGTGCCAAACTCATTGATTTTGGTTCCGGTGCCCTGCTTCATGATGAAC
CATATACCGACTTTGATGGAACACGGGTGTACAGCCCCCCTGAGTGGATCTCCCGTCACCAGTACCATGCCCTCCCGGCC
ACGGTTTGGTCACTGGGCATCCTCCTCTATGATATGGTATGTGGGGATATCCCGTTCGAGAAGGACCAGGAGATTCTGGA
GGCTGAGCTCCACTTCCCAGCCCATGTCTCTTCTGACTGCAGTGCCCTAATTCGCCGATGCCTGGCCTCCAAACCATCTG
AGCGCCCTTCGCGTGGAGGAGATCCTGATGGACCCCTGGATGAAGGCAGCA

Alignment

ORF - retro_sara_223 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 98.27 %
• Parental protein coverage: 90.55 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  IKVIPRNRVLDWSPLPDSGTCPLEVALLWKVGAGGGHPGVIRLLDWFETAEGFMLVLERPLPAQDLFDYI
          IKVI.RNRVLDWSPLPDSGTCPLEVALLWKVGAGGGHPGVIRLLDWFETAEGFMLVLERPLPAQDLFDYI
Retrocopy IKVISRNRVLDWSPLPDSGTCPLEVALLWKVGAGGGHPGVIRLLDWFETAEGFMLVLERPLPAQDLFDYI

Parental  TEQGPLGENRSRSLFAQVVAAVRHCHARGVVHRDIKDENILMDLRRGCAKLIDFGSGALLHDEPYTDFDG
          TEQGPLGENRSRSLFAQVVAAV.HCHARGVVHRDIKDENILMDLRRGCAKLIDFGSGALLHDEPYTDFDG
Retrocopy TEQGPLGENRSRSLFAQVVAAVQHCHARGVVHRDIKDENILMDLRRGCAKLIDFGSGALLHDEPYTDFDG

Parental  TRVYSPPEWISRHQYHALPATVWSLGILLYDMVCGDIPFEKDQEILEAELHFPAHVSSDCSALIRRCLAS
          TRVYSPPEWISRHQYHALPATVWSLGILLYDMVCGDIPFEKDQEILEAELHFPAHVSSDCSALIRRCLAS
Retrocopy TRVYSPPEWISRHQYHALPATVWSLGILLYDMVCGDIPFEKDQEILEAELHFPAHVSSDCSALIRRCLAS

Parental  KPSERPS-LEEILMDPWMKAA
          KPSERPS..EEILMDPWMKAA
Retrocopy KPSERPS>VEEILMDPWMKAA

Legend:

• *: Stop codon
• >: Forward frameshift by one nucleotide
• <: Reverse frameshift by one nucleotide

Expression

RNA-Seq

Sorex araneus was not studied using RNA-Seq expression data.

ChIP-Seq

Sorex araneus was not studied using ChIP-Seq data.

EST

Sorex araneus was not studied using EST data.

TSS

Sorex araneus was not studied using FANTOM5 data.

Lab

retro_sara_223 was not experimentally validated.

Homology

Retrocopy orthology:

Sorex araneus 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 5 parental genes, and 8 retrocopies.

Species	Parental gene accession	Retrocopies number
Echinops telfairi	ENSETEG00000007968	1 retrocopy	retro_etel_401,
Mus musculus	ENSMUSG00000031155	2 retrocopies	retro_mmus_2005, retro_mmus_3178,
Oryctolagus cuniculus	ENSOCUG00000015757	1 retrocopy	retro_ocun_1279,
Otolemur garnettii	ENSOGAG00000009613	1 retrocopy	retro_ogar_3049,
Sorex araneus	ENSSARG00000008832	3 retrocopies	retro_sara_222, retro_sara_223 , retro_sara_395,