RetrogeneDB ID: retro_trub_46

Retrocopy location

• Organism: Fugu rubripes (Takifugu rubripes)
• Coordinates: scaffold_77:845795..846910(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSTRUG00000012705
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: IFT52
• Ensembl ID: ENSTRUG00000014953
• Aliases: None
• Description: None

Sequence

>retro_trub_46
CAGTGTGACGCAGTGGCCTTCAATGCTTCCAAACGCGAGTTGTTTACTATCAACTCCAGGTACAAATCCATGCAGCGCAG
GCTGAGAGTGCAGTGGAGCGTCCAAAGCATGAGCGGCACGCTGTCACTGGAGAGACTGAAGAGGGTCAGGTTGTGGATAA
CTGTTGGACCAAGGGAGAAGTTCACAGCGTCAGAGCTGGAGGTGTTGAAGGAATACCTGGATGGGGGAGGACATGTGATG
GTTTTGCTTGGTGAAGGAGGAGAAACCAAATATAAGACCAACATCAACTTTCTCCTGGAGGAACTTGGAATAGTGGTCAA
CAAAGACGCGGTTGTGAGGAACGTGTACCACAGGTACTTGCATCCCAAAGAGGCACTTGTGTCTGACGGTGTGTTGAATA
GAGAAATTAGTCGAGCTGCCGATAAAGAGGTCAAGGGAACCTTTGAGGAGCCTCCTGGAAATGACCCAAAGGCTCTGGCG
TTTCTATATCCATACGGAGCCACGTTGAATGTGATGAAACCTGCTGTGGCGGTTCTCTCCACTGGTTCACTGTGCTTCCC
TTTCAACCGGCCTGTGATGGCCTTCCGTGAAGGTAAGGGGACTGGAAAACTGGTCGTGCTGGGTTCCTGCCACATGTTCA
GCGATCAATACATAGACAAAGAGGAAAACAGCAAAATCCTGGACGCTGTCCTCCAGTGGATCATGACGGATGACGCTGGC
ATGAACGGGACTGACGCCGCAGTGCCGGCGATTTCAGAATACACCATGATACCGGACACTCAGGTCCTGTCAGAGAAGCT
CCAGCTGTGTTTCCAGCACAACGAGGACCATTCCAGAATTTCACGTCTCTTTTCGATATGTCACTGTTTAACTTTTCTTC
TGCGTCCCTACCCCGCATCGTCAGCGCTTACAAGGAGCTTAACGTCAAATACGAGCCGCTCCACCGGGCGATCAGGCCAA
ACTTTGAGGCTCTGCTGCCTCCGCTTCAGCCGGCCGTCTTCCCACCTATTATCAGAGATTTGTCTCCGCCTGTGTTGGAG
CAGTTCGACCTCGATGAAGCCTTTCCCTCTGACAGAGAAGACGCCAGTAACTCCACCGACGACAATTTCGAATTC

Alignment

ORF - retro_trub_46 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 70.63 %
• Parental protein coverage: 84.88 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  QCSLAVFNASKRELFTTNSGYKSMQKRLRAQWKIQSLKDELSPEKLKGVKLWITVGPREKFTASELEMLK
          QC....FNASKRELFT.NS.YKSMQ.RLR.QW..QS....LS.E.LK.V.LWITVGPREKFTASELE.LK
Retrocopy QCDAVAFNASKRELFTINSRYKSMQRRLRVQWSVQSMSGTLSLERLKRVRLWITVGPREKFTASELEVLK

Parental  DYMDGGGNVMVLLGEGGETKYETNINFLLEEFGIMVNNDVVVRNVYYKYLHPKEALVSDGVLNREISRAA
          .Y.DGGG.VMVLLGEGGETKY.TNINFLLEE.GI.VN.D.VVRNVY..YLHPKEALVSDGVLNREISRAA
Retrocopy EYLDGGGHVMVLLGEGGETKYKTNINFLLEELGIVVNKDAVVRNVYHRYLHPKEALVSDGVLNREISRAA

Parental  GKMATGTYDETLENDAKALTFLYPYGATLNVMKPAVAVLSTGSECFPFNRPILAFHQGKETGKLAVLGSC
          .K...GT..E...ND.KAL.FLYPYGATLNVMKPAVAVLSTGS.CFPFNRP..AF..GK.TGKL.VLGSC
Retrocopy DKEVKGTFEEPPGNDPKALAFLYPYGATLNVMKPAVAVLSTGSLCFPFNRPVMAFREGKGTGKLVVLGSC

Parental  HIFSDQYIDKEENSKLMDVVLQWLTTDSIEMNQIDAEEPEITEYTIIPDSKGLSEKLHVCLQDGEENPR-
          H.FSDQYIDKEENSK..D.VLQW..TD...MN..DA..P.I.EYT.IPD...LSEKL..C.Q..E...R.
Retrocopy HMFSDQYIDKEENSKILDAVLQWIMTDDAGMNGTDAAVPAISEYTMIPDTQVLSEKLQLCFQHNEDHSR<

Parental  DFTSLFNTSLFNLSSSLSLPDIISAYKELNVKYEPL-QLITPQFETPLPPLQPAVFPPAVRDLPPPMLDL
          .FTSLF..SLFN.SS..SLP.I.SAYKELNVKYEPL...I.P.FE..LPPLQPAVFPP..RDL.PP.L..
Retrocopy NFTSLFDMSLFNFSSA-SLPRIVSAYKELNVKYEPLHRAIRPNFEALLPPLQPAVFPPIIRDLSPPVLEQ

Parental  FDLDEAFSSEKVRLAQLTNKCTDDDLEF
          FDLDEAF.S........T....DD..EF
Retrocopy FDLDEAFPSDREDASNST----DDNFEF

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_46 retrocopy.

TSS

Takifugu rubripes was not studied using FANTOM5 data.

Lab

retro_trub_46 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_trub_46 has 0 orthologous retrocopies within teleost group .

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Parental genes homology:

Parental genes homology involve 5 parental genes, and 5 retrocopies.

Species	Parental gene accession	Retrocopies number
Cavia porcellus	ENSCPOG00000027175	1 retrocopy	retro_cpor_301,
Microcebus murinus	ENSMICG00000015182	1 retrocopy	retro_mmur_400,
Myotis lucifugus	ENSMLUG00000016664	1 retrocopy	retro_mluc_990,
Otolemur garnettii	ENSOGAG00000007699	1 retrocopy	retro_ogar_2343,
Takifugu rubripes	ENSTRUG00000014953	1 retrocopy	retro_trub_46 ,