RetrogeneDB ID: retro_sara_242

Retrocopy location

• Organism: Shrew (Sorex araneus)
• Coordinates: scaffold_129432:4638..5660(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: GPBP1L1
• Ensembl ID: ENSSARG00000004852
• Aliases: None
• Description: GC-rich promoter binding protein 1-like 1 [Source:HGNC Symbol;Acc:28843]

Sequence

>retro_sara_242
GGCTGTGCCTTTCAGGAAAAGCCTCCCACGGAGACTAGGGAAGAAAAGAAAGACAACAAAATGGAAAAGTTGCAGTTCGA
AGAAGAAGATTTTCCTTCTTTGAATCCAGAAGCTAGCAAACAGAATCAGCCATGCAGACCTATTGGGACCCCTTCTGGAG
TGTGGGAAAACCCACCTTGTGCCAAGCAATCCTCCAAGATGCTAGTCATCAAAAAAGTTTCCAAAGAAGATCCTACTGCT
GCCTTCTCTGCTGCATTCACCTCACCAGGATCTCACCATGAAAATGGAAACAAATCATCAACTATGGTTCCAAGTGTGTA
TAAGAATCTGGTTCCTAAGCCTGCACCACCCCCTTCCAAGCTCAGTGCATGGAAAGCTAACAGAATGGAACACAAGTCAG
GATCCCTTTCCTCTGGTTGGGAATCTGCATTTACCAGTCCAATCTCTGTTACCAAACCAGTAGTACTGGCTAGTGGCTCA
ATTCTGAGCTCTCCCAAAGAGAGTCCATCCAGCACCACTCCTCCCATTGAGATTAGCTCCTCTCTCCTGACCAAGTTGAC
CCGCTGAACTTCCGACAGGAAAAGTGAGTTCCTAAAGACTCTGAAGGATGACCGGAACGGAGACTTCTCAGAGAACAGAG
ACTGTGACCAACTGGAGGACAGCAGCACACTTGAACCAAAGGAAAATGGAGAGGAAGGCTGTAATCAGAATGGTCTTGCT
CACCCTGTAGAAGAAGAAAGGGAGGTCCTCTCACACTCTCTGGAAGCGGAACATCGATTACTGAAAGCAATGGGATGGCA
AGAATATCCTGAAAATGATGAGAATTGCCTTCCTCTCACAGAGGATGAACTCAAAGAGTTCCACATGAAGACAGAGCAGC
TGAGAAGAAATGACTTTGGAAAGAATGGCTTCTTGCAGAGCCGCAGTTCCAGCCTCTTCTCCCCTTGGAGAAGCACTTGT
AAAGCAGAGTTTGAGGACTCAGACGCAGAACCAGTAGCAGTGAAACATCAGATGATGATGCC

Alignment

ORF - retro_sara_242 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 95.36 %
• Parental protein coverage: 72.57 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  GCAFQEKPPTEIREEKKEDKMEKLQFEEEDFPSLNPEAGKQNQPCRPIGTPSGVWENPPCAKQSSKMLVI
          GCAFQEKPPTE.REEKK..KMEKLQFEEEDFPSLNPEA.KQNQPCRPIGTPSGVWENPPCAKQSSKMLVI
Retrocopy GCAFQEKPPTETREEKKDNKMEKLQFEEEDFPSLNPEASKQNQPCRPIGTPSGVWENPPCAKQSSKMLVI

Parental  KKVSKEDPTAAFSAAFTSPGSHHANGNKSSTMVPSVYKNLVPKPAPPPSKPSAWKANRMEHKSGSLSSGR
          KKVSKEDPTAAFSAAFTSPGSHH.NGNKSSTMVPSVYKNLVPKPAPPPSK.SAWKANRMEHKSGSLSSG.
Retrocopy KKVSKEDPTAAFSAAFTSPGSHHENGNKSSTMVPSVYKNLVPKPAPPPSKLSAWKANRMEHKSGSLSSGW

Parental  ESAFTSPISVTKPVVLASGSILSSPKESPSSTTPPIEISSSRLTKLTRRTSDRKSEFLKTLKDDRNGDFS
          ESAFTSPISVTKPVVLASGSILSSPKESPSSTTPPIEISSS.LTKLTR.TSDRKSEFLKTLKDDRNGDFS
Retrocopy ESAFTSPISVTKPVVLASGSILSSPKESPSSTTPPIEISSSLLTKLTR*TSDRKSEFLKTLKDDRNGDFS

Parental  ENRDCDKVEDLEDSSTLEPKENGEEGCHQNGLAHPVEEEREVLSHSLEAEHRLLKAMGWQEYPENDENCL
          ENRDCD....LEDSSTLEPKENGEEGC.QNGLAHPVEEEREVLSHSLEAEHRLLKAMGWQEYPENDENCL
Retrocopy ENRDCDQ---LEDSSTLEPKENGEEGCNQNGLAHPVEEEREVLSHSLEAEHRLLKAMGWQEYPENDENCL

Parental  PLTEDELKEFHMKTEQLRRNGFGKNGFLQSRSSSLFSPWRSTCKAEFEDSDAE-TSSSETSDDDA
          PLTEDELKEFHMKTEQLRRN.FGKNGFLQSRSSSLFSPWRSTCKAEFEDSDAE.TSSSETSDDDA
Retrocopy PLTEDELKEFHMKTEQLRRNDFGKNGFLQSRSSSLFSPWRSTCKAEFEDSDAE<TSSSETSDDDA

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_242 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.

---

Parental genes homology:

Parental genes homology involve 5 parental genes, and 6 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000010454	1 retrocopy	retro_chof_53,
Myotis lucifugus	ENSMLUG00000012432	2 retrocopies	retro_mluc_211, retro_mluc_834,
Rattus norvegicus	ENSRNOG00000037595	1 retrocopy	retro_rnor_390,
Sorex araneus	ENSSARG00000004852	1 retrocopy	retro_sara_242 ,
Tursiops truncatus	ENSTTRG00000012202	1 retrocopy	retro_ttru_1355,