RetrogeneDB ID: retro_olat_12

Retrocopy location

• Organism: Medaka (Oryzias latipes)
• Coordinates: 5:11229730..11230321(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSORLG00000006130
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: LSM12 (2 of 2)
• Ensembl ID: ENSORLG00000011310
• Aliases: None
• Description: LSM12 homolog (S. cerevisiae) [Source:HGNC Symbol;Acc:26407]

Sequence

>retro_olat_12
ATGGCGGCTCCTGGACCGGGGGAGTATTTTAGTGTCGGGAGCCATGTCTCTTGCCTCACCTGCCTAGGCCAACGTCTGCA
AGGAGAAGTTGTCGCATTTGATTACCAGTCCAAGATGTTAACTTTGAAATGTGCTTCCTCCAGTGGCAAGCCAAACCTGC
ACGACGTCATCCTGATCAACTTAGCCTACGTTTCTGAAGTGGACATAATTAATGACCGCACTGAGACTCCTCCTCCACTA
GCATCACTGAATGTTAGCAAGCTTGCCAATCGAGCACGGACAGAAAAGGAGGACAAGCTGTCCCAAGCCTATGCAATCAG
TGCTGGGGTTTCTGTGGAGGGCCAACAGCTATTCCAGACTATTCATAAAACCATCAAAGACTGTAAATGGCAGGAGAAGA
ACATTATTGTGATGGACGATGTCATTATCTCACCGCCTTACCAGGTCGAGAACTGCAAAGGCAAAGAGGGAAGCGCTTTA
AGTCATGTACGCAAAATAGTTGAGAAACATTTTAGAGACCTGGAAAGTCAGAAGTCCATGCAACGTTCACAAGCACAGCA
AACACAGAAGGACTCCACTTTATCATCTTGA

Alignment

ORF - retro_olat_12 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 100.0 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MAAPGPGEYFSVGSHVSCLTCLGQRLQGEVVAFDYQSKMLTLKCASSSGKPNLHDVILINLAYVSEVDII
          MAAPGPGEYFSVGSHVSCLTCLGQRLQGEVVAFDYQSKMLTLKCASSSGKPNLHDVILINLAYVSEVDII
Retrocopy MAAPGPGEYFSVGSHVSCLTCLGQRLQGEVVAFDYQSKMLTLKCASSSGKPNLHDVILINLAYVSEVDII

Parental  NDRTETPPPLASLNVSKLANRARTEKEDKLSQAYAISAGVSVEGQQLFQTIHKTIKDCKWQEKNIIVMDD
          NDRTETPPPLASLNVSKLANRARTEKEDKLSQAYAISAGVSVEGQQLFQTIHKTIKDCKWQEKNIIVMDD
Retrocopy NDRTETPPPLASLNVSKLANRARTEKEDKLSQAYAISAGVSVEGQQLFQTIHKTIKDCKWQEKNIIVMDD

Parental  VIISPPYQVENCKGKEGSALSHVRKIVEKHFRDLESQKSMQRSQAQQTQKDSTLSS
          VIISPPYQVENCKGKEGSALSHVRKIVEKHFRDLESQKSMQRSQAQQTQKDSTLSS
Retrocopy VIISPPYQVENCKGKEGSALSHVRKIVEKHFRDLESQKSMQRSQAQQTQKDSTLSS

Legend:

• *: Stop codon
• >: Forward frameshift by one nucleotide
• <: Reverse frameshift by one nucleotide

Expression

RNA-Seq

Oryzias latipes was not studied using RNA-Seq expression data.

ChIP-Seq

Oryzias latipes was not studied using ChIP-Seq data.

EST

1 EST(s) were mapped to retro_olat_12 retrocopy

EST ID	Start	End	Identity	Match	Mis-match	Score
BJ922675	11229962	11230135	100	172	0	172

TSS

Oryzias latipes was not studied using FANTOM5 data.

Lab

retro_olat_12 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_olat_12 has 0 orthologous retrocopies within teleost group .

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Parental genes homology:

Parental genes homology involve 18 parental genes, and 21 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000014379	2 retrocopies	retro_cfam_1843, retro_cfam_312,
Choloepus hoffmanni	ENSCHOG00000001198	1 retrocopy	retro_chof_1429,
Dipodomys ordii	ENSDORG00000016381	1 retrocopy	retro_dord_596,
Erinaceus europaeus	ENSEEUG00000002419	1 retrocopy	retro_eeur_603,
Echinops telfairi	ENSETEG00000008374	1 retrocopy	retro_etel_21,
Felis catus	ENSFCAG00000029083	1 retrocopy	retro_fcat_787,
Homo sapiens	ENSG00000161654	1 retrocopy	retro_hsap_4041,
Loxodonta africana	ENSLAFG00000005202	1 retrocopy	retro_lafr_906,
Macropus eugenii	ENSMEUG00000007501	1 retrocopy	retro_meug_1462,
Myotis lucifugus	ENSMLUG00000006391	1 retrocopy	retro_mluc_2205,
Macaca mulatta	ENSMMUG00000006804	1 retrocopy	retro_mmul_3,
Mus musculus	ENSMUSG00000020922	1 retrocopy	retro_mmus_2683,
Otolemur garnettii	ENSOGAG00000010489	2 retrocopies	retro_ogar_1771, retro_ogar_2447,
Oryzias latipes	ENSORLG00000011310	1 retrocopy	retro_olat_12 ,
Pteropus vampyrus	ENSPVAG00000013706	1 retrocopy	retro_pvam_172,
Rattus norvegicus	ENSRNOG00000020894	1 retrocopy	retro_rnor_2845,
Tupaia belangeri	ENSTBEG00000012523	2 retrocopies	retro_tbel_3062, retro_tbel_60,
Vicugna pacos	ENSVPAG00000011145	1 retrocopy	retro_vpac_627,