RetrogeneDB ID: retro_sara_651

Retrocopy location

• Organism: Shrew (Sorex araneus)
• Coordinates: scaffold_253138:297510..298186(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: HDAC2
• Ensembl ID: ENSSARG00000000354
• Aliases: None
• Description: histone deacetylase 2 [Source:HGNC Symbol;Acc:4853]

Sequence

>retro_sara_651
AGGCCCCATAAAGCCACTGCTGAAGAAATGACAAAATACCACAGTGATGAATACATCAAATTTCTACGTTCAATAAGACC
AGATAACATGTCTGAGTATAGTAAGCCGATGCAGAGATTTAATGTTGCGGAGGATTGTCCAGTGTTTGATGGACTCTTTG
AGTTTTGTCAGCTCTCAACTGGTGGCTCAGTTGCTGGGGCTGTGAAGTTAAACCGACAACAAACTGATATGGCTGTTAAC
TGGGCTGGGAGGATTACATCATGCTAAGAAATCAGAAGCATCAGGATTCTGTTACGTTAATGATATTGTGCTTGCCATCC
TTGAATTACTAAAGTATCATCAGAGAGTCTTATATATCGATATTGATATTCATCATGGTGATGGTGTTGAAGAAGCATTT
TATACAACAGATCGTCTGATGACTGTATCTTTCCATAAGTATGGGGAATACTTTCCTGGTACTGGAGACTTGAGGGATAT
TGGTGCAGGAAAAGGCAAATACTATGCTGTCAACTTTCCAATGAGAGATGGTATAGATGATGAGTCATATGGACAGATAT
TTAAGCCTATCATCTCAAAGGTTATGGAGATGTATCAACCTAGTGCTGTGGTGTTACAGTGTGGTGCTGATTCACTATCT
GGTGATAGACTTGGTTGCTTCAATCTGACTGTCAAA

Alignment

ORF - retro_sara_651 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 98.23 %
• Parental protein coverage: 52.33 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  RPHKATAEEMTKYHSDEYIKFLRSIRPDNMSEYSKQMQRFNVGEDCPVFDGLFEFCQLSTGGSVAGAVKL
          RPHKATAEEMTKYHSDEYIKFLRSIRPDNMSEYSK.MQRFNV.EDCPVFDGLFEFCQLSTGGSVAGAVKL
Retrocopy RPHKATAEEMTKYHSDEYIKFLRSIRPDNMSEYSKPMQRFNVAEDCPVFDGLFEFCQLSTGGSVAGAVKL

Parental  NRQQTDMAVNWAG-GLHHAKKSEASGFCYVNDIVLAILELLKYHQRVLYIDIDIHHGDGVEEAFYTTDRV
          NRQQTDMAVNWAG.GLHHAKKSEASGFCYVNDIVLAILELLKYHQRVLYIDIDIHHGDGVEEAFYTTDR.
Retrocopy NRQQTDMAVNWAG>GLHHAKKSEASGFCYVNDIVLAILELLKYHQRVLYIDIDIHHGDGVEEAFYTTDRL

Parental  MTVSFHKYGEYFPGTGDLRDIGAGKGKYYAVNFPMRDGIDDESYGQIFKPIISKVMEMYQPSAVVLQCGA
          MTVSFHKYGEYFPGTGDLRDIGAGKGKYYAVNFPMRDGIDDESYGQIFKPIISKVMEMYQPSAVVLQCGA
Retrocopy MTVSFHKYGEYFPGTGDLRDIGAGKGKYYAVNFPMRDGIDDESYGQIFKPIISKVMEMYQPSAVVLQCGA

Parental  DSLSGDRLGCFNLTVK
          DSLSGDRLGCFNLTVK
Retrocopy DSLSGDRLGCFNLTVK

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_651 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 10 parental genes, and 16 retrocopies.

Species	Parental gene accession	Retrocopies number
Ciona intestinalis	ENSCING00000002649	1 retrocopy	retro_cint_18,
Echinops telfairi	ENSETEG00000008468	1 retrocopy	retro_etel_488,
Myotis lucifugus	ENSMLUG00000003117	4 retrocopies	retro_mluc_1570, retro_mluc_225, retro_mluc_2548, retro_mluc_935,
Monodelphis domestica	ENSMODG00000017860	1 retrocopy	retro_mdom_597,
Ornithorhynchus anatinus	ENSOANG00000003631	1 retrocopy	retro_oana_79,
Pan troglodytes	ENSPTRG00000018519	1 retrocopy	retro_ptro_69,
Sorex araneus	ENSSARG00000000354	1 retrocopy	retro_sara_651 ,
Ictidomys tridecemlineatus	ENSSTOG00000012779	1 retrocopy	retro_itri_374,
Tarsius syrichta	ENSTSYG00000009363	4 retrocopies	retro_tsyr_1337, retro_tsyr_1355, retro_tsyr_681, retro_tsyr_765,
Tursiops truncatus	ENSTTRG00000015043	1 retrocopy	retro_ttru_462,