RetrogeneDB ID: retro_trub_16

Retrocopy location

• Organism: Fugu rubripes (Takifugu rubripes)
• Coordinates: scaffold_214:483898..485752(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSTRUG00000009479
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: FEM1C
• Ensembl ID: ENSTRUG00000012022
• Aliases: None
• Description: None

Sequence

>retro_trub_16
ATGGACATATCGACGGCGGTTTTCAACGCGGCCAGGGATGGTAAGCTGAAACTTATCCAGAAGTTGCTGAGCAACAAAAC
TCCTGAGGAACTAGAGACATTAGCCGAGGAGAAAACCCAGGGAGGCACACCTCTGTTGATCGCCTCTCGATACGGACATT
TAGAGGTGGTCGATTACCTCCTCGAACACTGTAAAGCCAATGTTGAACTCGGGGGGGCGGTCAACTTTGACGGCGAGACC
ATCGAAGGTGCTCCGCCGCTGTGGGCGGCATCGGCGGCCGGTCACCTCCCGGTGGTGAAGAGGCTACTGAAACGCGGAGC
CTCCGTCAACAATGCCACACTAACCAACTCGACGCCCCTGCGGGCCGCCTGCTTTGACGGGCATCTCGAGATAGTCCGAT
ATCTGGTGGACCACAGAGCCGACATGGAGGTGGCCAACCGCCACGGCCACACCTGCCTCATGATCTCGTGTTACAAGGGC
CACAAGGAGATCGCCAAGTTCCTGCTGGACCGAGGAGCTGATGTCAACCGCAAGAGCGTGAAGGGCAACACCGCCCTGCA
CGACTGCGCCGAGTCGGGGAGTCTTGACATCATGAAGATGCTGCTAAAGTGCGACGCTCAGATGGAAAGGGACGGGTACG
GCATGACCCCGCTCCTCGCTGCCAGCGTAACCGGTCACGCCAACATCGTGGTGTACCTCGTCCACCAGACGCGGACCTCC
AGAGAGGAACGCGTCGACGCTCTCGAGCTCCTCGGGGCGACGTTTGTGGACAAAAAGAGGGATCTGCTCGGTGCAATGAG
GTACTGGAGATGGGCCATGGAGCTGAGGCACCCAGTGTATATCACCGAATCCCTGGCCAAGCCCCCGCCTGGTCCTCCCG
TCCCAGCATACGGCTGCGCTCAGGAGGTGAACACCGTAGAGGAACTCGAGGCTTTGATCACAGACCCCGATGAAATGAGG
ATGCAGGCTTTGCTGATCCGCGAGCGCATCCTCGGACCTTCTCATCCGGACACTTCTTATTATATCCGCTACAGGGGAGC
CGTGTACGCCGACTCGGGCAACTTTGAGCGGTGCATCAGCCTGTGGAAGTATGCTTTAGACATGCAGCAGAGCAACCTCG
ACCCTCTCAGTCCAATGACGGCCTCCAGTTTCCTCTCCTTCGCAGAGCTCTTCTCTTTTGTCCTTCAGGACCGCGCCAAG
GGCACCATGTCCACGCGCGTCACCTTCTCCGACCTGATGACGGTGCTGGGGAAAAGCGTGCGGGAAGTAGAGAGAGCGAT
GGCCCAGAACGGCAACCTGCCCGAAGCCTCCCAGTTCACCAAAGCGCTCTCCATCATCCTGCACCTCATCTTCCTCCTGG
AGAAGCTGGACTGTAGTCCGGAGCAGGAGCACCAGAAGAAGCACACCTTGTACCGCCTGCTGAAGCTGAATCCCCGCGGC
CGCAGCGGCTTCACCCCCCTCCACATGGCCGTAGACAAAGAGACCACGTCGGTGGGCCGCTACCCCGTGGGTCGCTTCCC
CTCTCAGGCAGTGGCGGCGGTACTCCTAGAATGCGGCGCCGACATCGATTCCCGGGACTACGACAACAACACGCCGCTGC
ACGTCGCTGCTAGCAACGGCTGCCCGGAGATCATGGCTCTGCTCATAAAGGCCGGGGCTCATTTCGACGCGAAGAACGCC
CAGAGGAAGATGGCCTACGAGCTGCTGGACGAGCCGAGCAGCGGCCACCCCGCCATCTACCCGCTGAACTGCGTCACCCT
TCAGTGCCTGGCGGCTCGTGCCATCGAGAAGCACAGACTCCCCTACAGGGGGCTCATTTCTGAGGAGATGGAGGCTTTCA
TTGAGCTGCACTGA

Alignment

ORF - retro_trub_16 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 63.89 %
• Parental protein coverage: 62.2 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  VHGCLTLFKILLSPQQTRHEARIDALELLGATFVDKKRDLLGALKYWKRAMDLRY-MDSNNIVQKPEPKQ
          V.G.......L.....T..E.R.DALELLGATFVDKKRDLLGA..YW..AM.LR..........KP.P..
Retrocopy VTGHANIVVYLVHQTRTSREERVDALELLGATFVDKKRDLLGAMRYWRWAMELRHPVYITESLAKPPPGP

Parental  LIMAYDYAKEVTNGEELDGLISDPDEMRMQALLIRERILGPQHPDTSYYIRYRGAVYADSGNFERCINLW
          ...AY..A.EV...EEL..LI.DPDEMRMQALLIRERILGP.HPDTSYYIRYRGAVYADSGNFERCI.LW
Retrocopy PVPAYGCAQEVNTVEELEALITDPDEMRMQALLIRERILGPSHPDTSYYIRYRGAVYADSGNFERCISLW

Parental  KYALDMQQSNLDPLSPMTASSLLSFAELFSFMLQDRAKGLLGTSISFEDLMGILSKGVLEIERAVKHSGP
          KYALDMQQSNLDPLSPMTASS.LSFAELFSF.LQDRAKG...T...F.DLM..L.K.V.E.ERA....G.
Retrocopy KYALDMQQSNLDPLSPMTASSFLSFAELFSFVLQDRAKGTMSTRVTFSDLMTVLGKSVREVERAMAQNGN

Parental  TALDPAQLSKALSIILHLICLLEKVPCTAEQDHFKKETIYRFLKLQPCGKNGYSPLHLAVDRNTTCVGRY
          ......Q..KALSIILHLI.LLEK..C..EQ.H.KK.T.YR.LKL.P.G..G..PLH.AVD..TT.VGRY
Retrocopy LP-EASQFTKALSIILHLIFLLEKLDCSPEQEHQKKHTLYRLLKLNPRGRSGFTPLHMAVDKETTSVGRY

Parental  PVCKFPSLTVASILLECGADVNSRDNDDNSPLHVAASNGHPDIMNLLISSGSHFDSTNAFQQTACDLLDA
          PV..FPS..VA..LLECGAD..SRD.D.N.PLHVAASNG.P.IM.LLI..G.HFD..NA....A..LLD.
Retrocopy PVGRFPSQAVAAVLLECGADIDSRDYDNNTPLHVAASNGCPEIMALLIKAGAHFDAKNAQRKMAYELLDE

Parental  KELSRNVIQPINHTTLQCLAARTIIKHRLNYRGNIPEKLEAFVLLH
          .......I.P.N..TLQCLAAR.I.KHRL.YRG.I.E..EAF..LH
Retrocopy PSSGHPAIYPLNCVTLQCLAARAIEKHRLPYRGLISEEMEAFIELH

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_16 retrocopy.

TSS

Takifugu rubripes was not studied using FANTOM5 data.

Lab

retro_trub_16 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_trub_16 has 3 orthologous retrocopies within teleost group .

Species	RetrogeneDB ID
Gasterosteus aculeatus	retro_gacu_12
Oryzias latipes	retro_olat_3
Tetraodon nigroviridis	retro_tnig_27

---

Parental genes homology:

Parental genes homology involve 7 parental genes, and 7 retrocopies.

Species	Parental gene accession	Retrocopies number
Gasterosteus aculeatus	ENSGACG00000007406	1 retrocopy	retro_gacu_12,
Gadus morhua	ENSGMOG00000005806	1 retrocopy	retro_gmor_12,
Oreochromis niloticus	ENSONIG00000015041	1 retrocopy	retro_onil_20,
Oryzias latipes	ENSORLG00000004946	1 retrocopy	retro_olat_3,
Tetraodon nigroviridis	ENSTNIG00000003195	1 retrocopy	retro_tnig_27,
Takifugu rubripes	ENSTRUG00000012022	1 retrocopy	retro_trub_16 ,
Xiphophorus maculatus	ENSXMAG00000015297	1 retrocopy	retro_xmac_5,