RetrogeneDB ID: retro_sara_616

Retrocopy location

• Organism: Shrew (Sorex araneus)
• Coordinates: scaffold_241225:6926..8940(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSSARG00000000466
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: DDX42
• Ensembl ID: ENSSARG00000009847
• Aliases: None
• Description: DEAD (Asp-Glu-Ala-Asp) box helicase 42 [Source:HGNC Symbol;Acc:18676]

Sequence

>retro_sara_616
ATGAACTGGAATAAAGGTGGCCCTGGCACTAAGAGGGGATTTGGCTTTGGAGGTTTTGCCATTAGTGCTGGAAAGAAGGA
GGAACCCAAAACTTCCACAACAGTCCCATAGTGCCTTTGGGTCAACCAGCTCAGCGTCTGGGTTTGGAAAGTCAGCTCCA
CCACAGCTCCCTTCTTTCTATAAAATTGGATCTAAACGGGCCAACTTCGATGAAGAAAATGCGTATTTTGAAGATGAGGA
GGAAGACTCCAGCAATGTTGACTTACCTTACATTCCTGCTGAAAACTCGCCTACCCGCCAGCAATTCCATTCCAAGCCTG
CAGATTCTGACAGCGATGATGATCCCTTGGAGGCATTCATGGCTGAAGTGGAGGATCAGGCGGCTAGAGATATGAAGAGA
CTTGAAGACAAGGACAAGGAAAGAAAAAACGTAAAGGGTATTCGAGATGACATTGAAGAGGAAGATGACCAAGAAGCTTA
TTTTCGGTACATGGCAGAAAATCCAACTGCTGGTGTGGTTCAAGAGGAGGAGGAAGATAATTTGGAATATGATAGTGATG
GAAATCCAATTGCACCTTCCAAAAAAATCATTGATCCTCTTCCTCCCATTGATCATTCAGAGATTGATTATCCACCATTT
GAAAAAAATTTTTACAATGAACATGAAGAGATAACCAACCTCACACCACAGCAACTTATAGATCTCCGGCATAAGCTCAA
TCTTCGGGTCTCTGGTGCTGCACCTCCTCGACCAGGAAGTAGTTTTGCTCATTTTGGGTTTGATGAACAACTTATGCACC
AGATTCGGAAGTCTGAATATACACAGCCCACTCCAATACAGTGCCAGGGTGTGCCTGTTGCCTTAAGTGGTAGAGATATG
ATTGGCATTGCCAAAACAGGCAGTGGAAAAACTGCAGCCTTTATCTGGCCTATGTTGATTCACATAATGGACCAGAAGGA
ACTGGAGCCAGGTGATGGGCCAATTGCAGTGATTGTGTGTCCTACTAGGGAGTTGTGCCAACAGATCCATGCAGAATGTA
AACGGTTTGGGAAAGCATATAATCTTCGATCGGTGGCCGTGTATGGAGGCGGGAGCATGTGGGAGCAGGCCAAGGCCCTT
CAGGAAGGGGCAGAGATTGTTGTGTGTACCCCAGGTCGATTGATTGATCATGTGAAGAAGAAAGCCACCAATCTTCAGAG
AGTGTCTTACCTTGTGTTTGATGAAGCAGATAGAATGTTTGACATGGGATTTGAATATCAGGTGCGGTCCATTGCAAGTC
ATGTCCGTCCTGACAGACAGACTCTCTTATTCAGCGCAACTTTTCGGAAAAAAATTGAAAAATTGGCCCGAGACATCCTG
ATCGATCCTATTCGAGTCGTGCAGGGAGATATTGGAGAGGCAAATGAAGATGTGACACAGATTGTGGAAATTCTCCATTC
TGGGCCCAGCAAATGGAACTGGCTGACACGACGTCTGGTGGAGTTTACCTCTTCAGGAAGTGTCCTTCTGTTTGTGACTA
AGAAAGCCAATGCTGAAGAGCTAGCCAATAATCTTAAGCAGGAAGGTCATAACCTTGGGCTGCTCATTGGGGACATGGAT
CAGAGTGAAAGAAACAAGGTCATTTCAGACTTCAAGAAAAAGGACATTCCAGTCCTGGTTGCCACAGACGTTGCAGCCCG
TGGTCTGGACATCCCTTCTATTAAGACTGTCATTAACTATGATGTGGCTCGAGATATTGACACTCACACTCACAGAATTG
GCCGTACGGGACGAGCAGGGGAGAAAGGAGTTGCCTATACTTTGCTGACCCCTAAGGATAGCAATTTTGCTGGTGACCTT
GTCCGGAACTTGGAAGGGGCCAATCAGCATGTTTCTAAGGAACTTCTCGATCTGGCGATGCAGAATGCCTGGTTTCGGAA
ATCCCGCTTCAAAGGAGGGAAAGGCAAAAAGCTTAACATTGGTGGAGGTGGCAAATACGGCTACAGGGAGAGGCCTGGCC
TAGGCTCTGAGAAC

Alignment

ORF - retro_sara_616 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 98.96 %
• Parental protein coverage: 71.7 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MNWNKGGPGTKRGFGFGGFAISAGKKEEPK-LPQQSHSAFGSTSSASGFGKSAPPQLPSFYKIGSKRANF
          MNWNKGGPGTKRGFGFGGFAISAGKKEEPK.LPQQSHSAFGSTSSASGFGKSAPPQLPSFYKIGSKRANF
Retrocopy MNWNKGGPGTKRGFGFGGFAISAGKKEEPK>LPQQSHSAFGSTSSASGFGKSAPPQLPSFYKIGSKRANF

Parental  DEENAYFEDEEEDSSNVDLPYIPAENSPTRQQFHSKPADSDSDDDPLEAFMAEXXDQAARDMKRLEDKDK
          DEENAYFEDEEEDSSNVDLPYIPAENSPTRQQFHSKPADSDSDDDPLEAFMAE..DQAARDMKRLEDKDK
Retrocopy DEENAYFEDEEEDSSNVDLPYIPAENSPTRQQFHSKPADSDSDDDPLEAFMAEVEDQAARDMKRLEDKDK

Parental  ERKNVKGIRDDIEEEDDQEAYFRYMAENPTAGVVQEEEEDNLEYDSDGNPIAPSKKIIDPLPPIDHSEID
          ERKNVKGIRDDIEEEDDQEAYFRYMAENPTAGVVQEEEEDNLEYDSDGNPIAPSKKIIDPLPPIDHSEID
Retrocopy ERKNVKGIRDDIEEEDDQEAYFRYMAENPTAGVVQEEEEDNLEYDSDGNPIAPSKKIIDPLPPIDHSEID

Parental  YPPFEKNFYNEHEEITNLTPQQLIDLRHKLNLRVSGAAPPRPGSSFAHFGFDEQLMHQIRKSEYTQPTPI
          YPPFEKNFYNEHEEITNLTPQQLIDLRHKLNLRVSGAAPPRPGSSFAHFGFDEQLMHQIRKSEYTQPTPI
Retrocopy YPPFEKNFYNEHEEITNLTPQQLIDLRHKLNLRVSGAAPPRPGSSFAHFGFDEQLMHQIRKSEYTQPTPI

Parental  QCQGVPVALSGRDMIGIAKTGSGKTAAFIWPMLIHIMDQKELEPGDGPIAVIVCPTRELCQQIHAECKRF
          QCQGVPVALSGRDMIGIAKTGSGKTAAFIWPMLIHIMDQKELEPGDGPIAVIVCPTRELCQQIHAECKRF
Retrocopy QCQGVPVALSGRDMIGIAKTGSGKTAAFIWPMLIHIMDQKELEPGDGPIAVIVCPTRELCQQIHAECKRF

Parental  GKAYNLRSVAVYGGGSMWEQAKALQEGAEIVVCTPGRLIDHVKKKATNLQRVSYLVFDEADRMFDMGFEY
          GKAYNLRSVAVYGGGSMWEQAKALQEGAEIVVCTPGRLIDHVKKKATNLQRVSYLVFDEADRMFDMGFEY
Retrocopy GKAYNLRSVAVYGGGSMWEQAKALQEGAEIVVCTPGRLIDHVKKKATNLQRVSYLVFDEADRMFDMGFEY

Parental  QVRSIASHVRPDRQTLLFSATFRKKIEKLARDILIDPIRVVQGD-GEANEDVTQIVEILHSGPSKWNWLT
          QVRSIASHVRPDRQTLLFSATFRKKIEKLARDILIDPIRVVQGD.GEANEDVTQIVEILHSGPSKWNWLT
Retrocopy QVRSIASHVRPDRQTLLFSATFRKKIEKLARDILIDPIRVVQGDIGEANEDVTQIVEILHSGPSKWNWLT

Parental  RRLVEFTSSGSVLLFVTKKANAEELANNLKQEGHNLGLLHGDMDQSERNKVISDFKKKDIPVLVATDVAA
          RRLVEFTSSGSVLLFVTKKANAEELANNLKQEGHNLGLL.GDMDQSERNKVISDFKKKDIPVLVATDVAA
Retrocopy RRLVEFTSSGSVLLFVTKKANAEELANNLKQEGHNLGLLIGDMDQSERNKVISDFKKKDIPVLVATDVAA

Parental  RGLDIPSIKTVINYDVARDIDTHTHRIGRTGRAGEKGVAYTLLTPKDSNFAGDLVRNLEGANQHVSKELL
          RGLDIPSIKTVINYDVARDIDTHTHRIGRTGRAGEKGVAYTLLTPKDSNFAGDLVRNLEGANQHVSKELL
Retrocopy RGLDIPSIKTVINYDVARDIDTHTHRIGRTGRAGEKGVAYTLLTPKDSNFAGDLVRNLEGANQHVSKELL

Parental  DLAMQNAWFRKSRFKGGKGKKLNIGGGG-LGYRERPGLGSEN
          DLAMQNAWFRKSRFKGGKGKKLNIGGGG..GYRERPGLGSEN
Retrocopy DLAMQNAWFRKSRFKGGKGKKLNIGGGGKYGYRERPGLGSEN

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_616 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 1 parental gene, and 1 retrocopy.

Species	Parental gene accession	Retrocopies number
Sorex araneus	ENSSARG00000009847	1 retrocopy	retro_sara_616 ,