RetrogeneDB ID: retro_olat_11

Retrocopy location

• Organism: Medaka (Oryzias latipes)
• Coordinates: 23:20195678..20196422(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSORLG00000016386
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: TNNT1 (2 of 2)
• Ensembl ID: ENSORLG00000006832
• Aliases: None
• Description: troponin T type 1 (skeletal, slow) [Source:HGNC Symbol;Acc:11948]

Sequence

>retro_olat_11
GACTTTGAAGAAAGTGTTGAGTATGAAGAGGAAGAGGTTGAGGAAAAGAATGAGGAAGAGTCTAAATCCAAACACAAAAC
GGTTTATGTGCCTAACATGGTCCCTCCAAAGCTTCCCGATGGCGAGAAAGTGGATTTTGATGACCTCCACCGCAAGCGAC
TGGAGAAGGATTACAATGACCTGCAGAGTCTTATTGAGCTACATTTTTCCAGCCGTCAGAAGGAAGAGGAAGAGCTTATT
TCACTGCGCAACCGTATCGAAAGCCGCCGCGCCGACAGAGCTGAACAGCAGCGTGTCCGCGCGGAGCAGGAGCGCGAGCG
GCAAGCACGAGTGGCTGAGGAGAGGTCAAGGAGGGAGGAAGAGGCAGCCAAGCAGCGCGCCGAAGAGGATGCCAAGAAAA
AGATGATATTCTCCAACAAATCATTCGGTGGATACCTGCAGAAGGTCGACCAGAAGAAAGGCAAGAAGCTGACAGCTCGT
GAGGAGAAGAAGAAGGCCTTGATGGAGCGCAGGAAGCCGCTGAACATCGACCACCTGAACCAGGACAAGCTGCTAGAGAA
AGCTCAGGAACTCTGGCAGTGGCTCTACCAGCTGCATTCTGAGAAGTTTGATCTGGCTGAGAAGCTCAAGAAGCAAAAGT
ACGAAATCCACGTGCTTCGGAACCGAGTCAGTGACCACCAGAGGTTCTCCAAAACTCTCAAGAGCTCTCGTGGAGCCAAG
AGCAAGCCTGGTTCCAGGAAGTGA

Alignment

ORF - retro_olat_11 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 58.01 %
• Parental protein coverage: 91.63 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  EEDEEQGEEALCHLHPKEERPKPKPV-VPQIAAPKIPEGERVDFDDIHRKRMEKDLLELQTLIDVHFEQR
          EE..E..EE........E...K.K.V.VP....PK.P.GE.VDFDD.HRKR.EKD...LQ.LI..HF..R
Retrocopy EESVEYEEEEVEEKNEEESKSKHKTVYVPNMVPPKLPDGEKVDFDDLHRKRLEKDYNDLQSLIELHFSSR

Parental  KREEEELIGLKERIERRRAERAEQQRVRAEKERDRQTRLAAERQRKEDEEAKKRAEDEAKKKKVLSNMGA
          ..EEEELI.L..RIE.RRA.RAEQQRVRAE.ER.RQ.R.A.ER.R.E.E.AK.RAE..AKKK...SN...
Retrocopy QKEEEELISLRNRIESRRADRAEQQRVRAEQERERQARVAEERSRREEEAAKQRAEEDAKKKMIFSNKS-

Parental  HFGGFLAKVEQRRGKRQTGREIKKMTLAERRKPLAVENLREDGLREKAKELWEWIYELESEKFDLTEKMK
          .FGG.L.KV.Q..GK..T.RE.KK..L.ERRKPL....L..D.L.EKA.ELW.W.Y.L.SEKFDL.EK.K
Retrocopy -FGGYLQKVDQKKGKKLTAREEKKKALMERRKPLNIDHLNQDKLLEKAQELWQWLYQLHSEKFDLAEKLK

Parental  RQKYEINVLLNRIQHAQKFKK
          .QKYEI.VL.NR....Q.F.K
Retrocopy KQKYEIHVLRNRVSDHQRFSK

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

No EST(s) were mapped for retro_olat_11 retrocopy.

TSS

Oryzias latipes was not studied using FANTOM5 data.

Lab

retro_olat_11 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_olat_11 has 0 orthologous retrocopies within teleost group .

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Parental genes homology:

Parental genes homology involve 4 parental genes, and 4 retrocopies.

Species	Parental gene accession	Retrocopies number
Danio rerio	ENSDARG00000020610	1 retrocopy	retro_drer_9,
Oreochromis niloticus	ENSONIG00000012310	1 retrocopy	retro_onil_9,
Oryzias latipes	ENSORLG00000006832	1 retrocopy	retro_olat_11 ,
Takifugu rubripes	ENSTRUG00000011858	1 retrocopy	retro_trub_31,