RetrogeneDB ID: retro_trub_15

Retrocopy location

• Organism: Fugu rubripes (Takifugu rubripes)
• Coordinates: scaffold_89:871677..872253(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSTRUG00000009931
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSTRUG00000016201
• Aliases: None
• Description: None

Sequence

>retro_trub_15
ATGCAGACCATAAAGTGTGTGGTGGTTGGTGATGGGGCAGTAGGTAAAACCTGCCTACTCATCTCATACACAACTAATGC
CTTCCCAGAGGAGTACATACCCACTGTGTTTGACAACTACAGTGCTCAGATGAGCGTAGATGGCCGCACTGTTAGCCTTA
ACCTGTGGGACACAGCCGGCCAGGAGGAGTATGACCGCCTGCGTACTCTCTCTTATCCACAAACCAACGTCTTCATCATT
TGCTTTTCAATTGGCAGCCCCTCCTCTCATGCCAATGTCAGACACAAGTGGCATCCTGAGGTGTCTCACCACTGCCCCAA
TGTGCCCATCCTGCTGGTGGGCACCAAGAAGGACCTGAGGGGTGATACAGAAACAGTGAAGAAGCTGAAGGAGCAGGGCC
TGGCTCCTACCACCCACCAGCAGGGCAACGCCTTGGCCAAGCAGATTGGTGCCGTCAAGTACATGGAGTGCTCCGCTCTG
CTGCAGGATGGCGTCAGAGAGGTGTTTGCTGAAGCCGTGAGGGCAGTTTTGTATCCAGTAGCAAAAAAGAACCCCAAAAA
ATGCGTGCTGTTGTAA

Alignment

ORF - retro_trub_15 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 71.88 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MQAIKCVVVGDGAVGKTCLLISYTTNAFPGEYIPTVFDNYSANVMVDGKPVNLGLWDTAGQEDYDRLRPL
          MQ.IKCVVVGDGAVGKTCLLISYTTNAFP.EYIPTVFDNYSA...VDG..V.L.LWDTAGQE.YDRLR.L
Retrocopy MQTIKCVVVGDGAVGKTCLLISYTTNAFPEEYIPTVFDNYSAQMSVDGRTVSLNLWDTAGQEEYDRLRTL

Parental  SYPQTDVFLICFSLVSPASFENVRAKWYPEVRHHCPNTPIILVGTKLDLRDDKDTIEKLREKKLSPITYP
          SYPQT.VF.ICFS..SP.S..NVR.KW.PEV.HHCPN.PI.LVGTK.DLR.D..T..KL.E..L.P.T..
Retrocopy SYPQTNVFIICFSIGSPSSHANVRHKWHPEVSHHCPNVPILLVGTKKDLRGDTETVKKLKEQGLAPTTHQ

Parental  QGLAMAKEISAVKYLECSALTQRGLKTVFDEAIRAVLCPPPAKKKHKKCSLL
          QG.A.AK.I.AVKY.ECSAL.Q.G...VF.EA.RAVL..P.AKK..KKC.LL
Retrocopy QGNALAKQIGAVKYMECSALLQDGVREVFAEAVRAVLY-PVAKKNPKKCVLL

Legend:

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

Expression

RNA-Seq

Takifugu rubripes was not studied using RNA-Seq expression data.

ChIP-Seq

Takifugu rubripes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_trub_15 retrocopy.

TSS

Takifugu rubripes was not studied using FANTOM5 data.

Lab

retro_trub_15 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_trub_15 has 1 orthologous retrocopies within teleost group .

Species	RetrogeneDB ID
Tetraodon nigroviridis	retro_tnig_14

---

Parental genes homology:

Parental genes homology involve 13 parental genes, and 19 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000017364	1 retrocopy	retro_amel_1104,
Callithrix jacchus	ENSCJAG00000018194	1 retrocopy	retro_cjac_2687,
Cavia porcellus	ENSCPOG00000013861	1 retrocopy	retro_cpor_18,
Echinops telfairi	ENSETEG00000012902	3 retrocopies	retro_etel_1565, retro_etel_1645, retro_etel_42,
Felis catus	ENSFCAG00000011671	1 retrocopy	retro_fcat_431,
Macropus eugenii	ENSMEUG00000006196	1 retrocopy	retro_meug_201,
Otolemur garnettii	ENSOGAG00000012467	1 retrocopy	retro_ogar_2140,
Oreochromis niloticus	ENSONIG00000017151	1 retrocopy	retro_onil_34,
Procavia capensis	ENSPCAG00000009949	1 retrocopy	retro_pcap_16,
Pongo abelii	ENSPPYG00000008763	2 retrocopies	retro_pabe_1047, retro_pabe_2546,
Tupaia belangeri	ENSTBEG00000007272	4 retrocopies	retro_tbel_1796, retro_tbel_2564, retro_tbel_4296, retro_tbel_9,
Takifugu rubripes	ENSTRUG00000004543	1 retrocopy	retro_trub_12,
Takifugu rubripes	ENSTRUG00000016201	1 retrocopy	retro_trub_15 ,