RetrogeneDB ID: retro_sara_415

Retrocopy location

• Organism: Shrew (Sorex araneus)
• Coordinates: scaffold_196446:18850..19849(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: KARS
• Ensembl ID: ENSSARG00000011493
• Aliases: None
• Description: lysyl-tRNA synthetase [Source:HGNC Symbol;Acc:6215]

Sequence

>retro_sara_415
GAGCTAAAGCGCCGCTTGAAAGCCGAGAAGAAAATAGCGGAGAAGGAGGCCAAGCAGAAGGAGCTCAGTGAGAAGCAGCT
GGGCCAGGCCACAGCTGCGGCCACCAACCACACCACTGACAATGGTGTGGGCGCTGAGGAGGAGACCCTGGACCCCAACC
AATACTACAAGATCCGCAGTCAAGCAGTCCACCAACTGAAGGTCAGTGGGGAAGACCCTTACCCACACAAGTTCCACGTA
GATGTCTCGCTCACTCACTTCATCCAGGAATACAGTCACCTGCAGCTTGGAGACCACCTGACAGACATCACTTTGAGGGT
GGCAGGTAGAATCCATGCGAAAAGAGCTTCCGGGGGAAAGCTCATCTTCTATGACCTTCGAGGAGAGGGGGTGAAATTGC
AAGTCATGGCCAACTCCAGGAATTATAAATCAGAAGAAGAATTTGTTCGTATCAACAACAAGCTTCGTCGGGGAGACATA
ATTGGAGTTCAGGGGAACCCTGGGAAAACCAAGAAGGGCGAGCTGAGCATCATCCCGTACGAGATCACTCTGCTGTCGCC
TTGCTTGCACATGTTGCCGCATCTTCACTTTGGCCTCAAAGACAAGGAAACCCGGTATCGACAGAGGTACTTGGACCTGA
TCCTGAATGACTTCGTGAGGCAAAAGTTTATCATCCGCTCCAAGATCATCACGTATATAAGAAGTTTCTTGGATGAGTTG
GGATTCCTAGAGATCGAAACGCCCATGATGAACATCATCCCAGGAGGAGCTGTGGCCAAGCCTTTCATCACCTACCGCAA
TGAGCTGGACATGAATCTGTACATGAGAATTGCTCCAGAACTCTACCATAAGATGCTGGTGGTTGGTGGCATCAACCGGG
TTTATGAGATCGGACGTCAGTTCCGGAATGAAGGCATCGACTTGACACACAATCCCGAGTTCACCACGTGTGAGTTCTAC
ATGGCCTATGCCTACTACCACGACCTCATGGAGATCACG

Alignment

ORF - retro_sara_415 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 98.5 %
• Parental protein coverage: 57.81 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  ELKRRLKAEKKVAEKEAKQKELSEKQLGQATAAATNHTTDNGVGAEEETLDPNQYYKIRSQAVHQLKVSG
          ELKRRLKAEKK.AEKEAKQKELSEKQLGQATAAATNHTTDNGVGAEEETLDPNQYYKIRSQAVHQLKVSG
Retrocopy ELKRRLKAEKKIAEKEAKQKELSEKQLGQATAAATNHTTDNGVGAEEETLDPNQYYKIRSQAVHQLKVSG

Parental  EDPYPHKFHVDVSLTHFIQEYSHLQPGDHLTDITLRVAGRIHAKRASGGKLIFYDLRGEGVKLQVMANSR
          EDPYPHKFHVDVSLTHFIQEYSHLQ.GDHLTDITLRVAGRIHAKRASGGKLIFYDLRGEGVKLQVMANSR
Retrocopy EDPYPHKFHVDVSLTHFIQEYSHLQLGDHLTDITLRVAGRIHAKRASGGKLIFYDLRGEGVKLQVMANSR

Parental  NYKSEEEFVRINNKLRRGDIIGVQGNPGKTKKGELSIIPYEITLLSPCLHMLPHLHFGLKDKETRYRQRY
          NYKSEEEFVRINNKLRRGDIIGVQGNPGKTKKGELSIIPYEITLLSPCLHMLPHLHFGLKDKETRYRQRY
Retrocopy NYKSEEEFVRINNKLRRGDIIGVQGNPGKTKKGELSIIPYEITLLSPCLHMLPHLHFGLKDKETRYRQRY

Parental  LDLILNDFVRQKFIIRSKIITYIRSFLDELGFLEIETPMMNIIPGGAVAKPFITYHNELDMNLYMRIAPE
          LDLILNDFVRQKFIIRSKIITYIRSFLDELGFLEIETPMMNIIPGGAVAKPFITY.NELDMNLYMRIAPE
Retrocopy LDLILNDFVRQKFIIRSKIITYIRSFLDELGFLEIETPMMNIIPGGAVAKPFITYRNELDMNLYMRIAPE

Parental  LYHKMLVVGGIDRVYEIGRQFRNEGIDLTHNPEFTTCEFYMAYADYHDLMEIT
          LYHKMLVVGGI.RVYEIGRQFRNEGIDLTHNPEFTTCEFYMAYA.YHDLMEIT
Retrocopy LYHKMLVVGGINRVYEIGRQFRNEGIDLTHNPEFTTCEFYMAYAYYHDLMEIT

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_415 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 10 parental genes, and 19 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000013447	1 retrocopy	retro_chof_2324,
Callithrix jacchus	ENSCJAG00000014213	2 retrocopies	retro_cjac_4104, retro_cjac_608,
Homo sapiens	ENSG00000065427	1 retrocopy	retro_hsap_1191,
Gorilla gorilla	ENSGGOG00000005515	1 retrocopy	retro_ggor_930,
Mus musculus	ENSMUSG00000031948	8 retrocopies	retro_mmus_3536, retro_mmus_3537, retro_mmus_3538, retro_mmus_3539, retro_mmus_3540, retro_mmus_3541, retro_mmus_3542, retro_mmus_3543,
Nomascus leucogenys	ENSNLEG00000013072	1 retrocopy	retro_nleu_2080,
Pongo abelii	ENSPPYG00000007567	1 retrocopy	retro_pabe_992,
Pan troglodytes	ENSPTRG00000008364	1 retrocopy	retro_ptro_3036,
Pteropus vampyrus	ENSPVAG00000006746	2 retrocopies	retro_pvam_1301, retro_pvam_723,
Sorex araneus	ENSSARG00000011493	1 retrocopy	retro_sara_415 ,