RetrogeneDB ID: retro_olat_34

Retrocopy location

• Organism: Medaka (Oryzias latipes)
• Coordinates: 2:18267279..18267666(+)
• Located in intron of: ENSORLG00000001749

Retrocopy information

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

Parental gene information

• Parental gene symbol: OLA.17735
• Ensembl ID: ENSORLG00000020272
• Aliases: None
• Description: None

Sequence

>retro_olat_34
CTCCCCCAGCATTATGTAAGTGAAAAGGAGTATTGCTGCAACAAGCAGAGGAACTCCAGAGTCGAACAGGGGGAACCAGA
GTCTCAACAGATTAAAGAGGAATATGAGGGACCGGAACCTGCACAGATGAAAGGGGAGCAAGAAGGACTCTACATCATTC
AGGTTGAAGAAGAGCTTGATCTGAAGCAGGAAACTGACACCTTGATAGTGACTCCTACAGATCTAAACAATCTGCAGAGC
TTTAATGTAACTGATAGTCAGGATGAAGAAGAAGGCCCACATGAAGAATCAACATCAACTACAGATGGAGAGACAGACCC
ACAGAACAAAGATCGGAGGAAGAGAAAAGACAGAAGTCCTGTCCAAAACGTGGACAGCTCTCACATG

Alignment

ORF - retro_olat_34 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 54.26 %
• Parental protein coverage: 55.02 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  LPQHWMTEEEDLCNQQRNFRVEQEEPEPPQIK---EEPDELCISQDEDQLDLKQETDTLMEIPTYEEYEN
          LPQH...E.E..CN.QRN.RVEQ.EPE..QIK...E.P...........L...Q....L...........
Retrocopy LPQHYVSEKEYCCNKQRNSRVEQGEPESQQIKEEYEGPEPAQMKGEQEGLYIIQVEEELDLKQETDTLIV

Parental  SEADLNNQQSFNVTDSQDQEGNQHEESTSTTDEETDPQNIDQRKRRDRRHVQSVDSSHM
          ...DLNN.QSFNVTDSQD.E...HEESTSTTD.ETDPQN.D.RKR.DR..VQ.VDSSHM
Retrocopy TPTDLNNLQSFNVTDSQDEEEGPHEESTSTTDGETDPQNKDRRKRKDRSPVQNVDSSHM

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_34 retrocopy.

TSS

Oryzias latipes was not studied using FANTOM5 data.

Lab

retro_olat_34 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_olat_34 has 0 orthologous retrocopies within teleost group .

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Parental genes homology:

Parental genes homology involve 3 parental genes, and 13 retrocopies.

Species	Parental gene accession	Retrocopies number
Oryzias latipes	ENSORLG00000018644	1 retrocopy	retro_olat_44,
Oryzias latipes	ENSORLG00000019703	11 retrocopies	retro_olat_39, retro_olat_45, retro_olat_46, retro_olat_47, retro_olat_49, retro_olat_50, retro_olat_52, retro_olat_54, retro_olat_58, retro_olat_60, retro_olat_63,
Oryzias latipes	ENSORLG00000020272	1 retrocopy	retro_olat_34 ,