RetrogeneDB ID: retro_sara_76

Retrocopy location

• Organism: Shrew (Sorex araneus)
• Coordinates: GeneScaffold_2145:87556..87851(-)
• Located in intron of: ENSSARG00000009713

Retrocopy information

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

Parental gene information

• Parental gene symbol: RPL36AL
• Ensembl ID: ENSSARG00000014178
• Aliases: None
• Description: ribosomal protein L36a-like [Source:HGNC Symbol;Acc:10346]

Sequence

>retro_sara_76
GAAACTCACTGCACTTTCTGTAAGAAATGTGGCAAACATCAGCTCCACCAAGTCACACGGTACAAGAAGGGCAAGGATTC
TCTGTATACCGAGGGAAAGCAGCGTCAAGACAGGAAGCAGAGGTCAGCCTAAGCCAATTTTCTGGGAAAGACTAAAACTA
CAAAGAAGATTGTGTTGAGACTTGAATGCGTGGAGCCCAGCTGCACATCCCCGACAATGCAGGCCATTAAGGGATGCAAA
CGTTTTTGAACCGGCAGGAGATTAAAAAAAGACAAAGGGACAAGTAATCCAGTTC

Alignment

ORF - retro_sara_76 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 64.65 %
• Parental protein coverage: 95. %
• Number of stop codons detected: 2
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  KTRRTFCKKCGKHQPHKVTQYKKGKDSLYAQGKRRDQSYSQT--PIFRKKAKTTKKIVLRLECVEPNCRS
          .T..TFCKKCGKHQ.H.VT.YKKGKDSLY..GK.R...........F..K.KTTKKIVLRLECVEP.C.S
Retrocopy ETHCTFCKKCGKHQLHQVTRYKKGKDSLYTEGKQRQDRKQRSA*ANFLGKTKTTKKIVLRLECVEPSCTS

Parental  KRMLAIKRCKH-FELGGD-KKRKGQVIQF
          ..M.AIK.CK..FE..GD.KK.KGQVIQF
Retrocopy PTMQAIKGCKR>FEPAGD*KKTKGQVIQF

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_76 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 9 parental genes, and 42 retrocopies.

Species	Parental gene accession	Retrocopies number
Anolis carolinensis	ENSACAG00000008503	1 retrocopy	retro_acar_98,
Dasypus novemcinctus	ENSDNOG00000015954	23 retrocopies	retro_dnov_1206, retro_dnov_1266, retro_dnov_1320, retro_dnov_1328, retro_dnov_1330, retro_dnov_1392, retro_dnov_1427, retro_dnov_1525, retro_dnov_1799, retro_dnov_1898, retro_dnov_227, retro_dnov_2302, retro_dnov_233, retro_dnov_2371, retro_dnov_243, retro_dnov_2488, retro_dnov_2503, retro_dnov_2587, retro_dnov_310, retro_dnov_596, retro_dnov_699, retro_dnov_871, retro_dnov_936,
Felis catus	ENSFCAG00000015397	3 retrocopies	retro_fcat_106, retro_fcat_25, retro_fcat_80,
Gorilla gorilla	ENSGGOG00000009460	6 retrocopies	retro_ggor_13, retro_ggor_152, retro_ggor_207, retro_ggor_208, retro_ggor_42, retro_ggor_5,
Monodelphis domestica	ENSMODG00000025578	2 retrocopies	retro_mdom_1878, retro_mdom_971,
Pteropus vampyrus	ENSPVAG00000001569	1 retrocopy	retro_pvam_17,
Rattus norvegicus	ENSRNOG00000011494	1 retrocopy	retro_rnor_259,
Sorex araneus	ENSSARG00000014178	4 retrocopies	retro_sara_146, retro_sara_488, retro_sara_617, retro_sara_76 ,
Tursiops truncatus	ENSTTRG00000012779	1 retrocopy	retro_ttru_5,