RetrogeneDB ID: retro_xmac_5

Retrocopy location

• Organism: Platyfish (Xiphophorus maculatus)
• Coordinates: JH556675.1:2378243..2380097(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSXMAG00000019982
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: fem1c
• Ensembl ID: ENSXMAG00000015297
• Aliases: None
• Description: fem-1 homolog c (C.elegans) [Source:ZFIN;Acc:ZDB-GENE-031008-3]

Sequence

>retro_xmac_5
ATGGATATAACCGTGGCGGTTTTTAACGCGGCCAGAGATGGTAAGCTGAAACTTATCCAGAAGTTGCTGAGCAACAAAAC
TCCAGAGGAGCTGGAGGCTTTAGCGGAGGAGAAAACCCAGGGCAGCACCGCGCTTCTCATAGCCTCTCGGTACGGACATT
TAGAGGTCGTAGACTACCTGCTCGAACATTGTAAAGCTAATGTTGAACTCGGGGGCTCGGTCAACTTTGACGGCGAGACT
ATCGAGGGGGCTCCACCGCTGTGGGCGGCTTCGGCAGCGGGTCACCTCCCCGTGGTGAAGACGCTGCTGAAACACGGAGC
CTCGGTAAACAACGCCACGCTAACGAACTCCACCCCGCTCCGAGCCGCTTGCTTCGACGGCCACCTAGAGATCGTTCGCT
ACCTGGTGGAGCACAGAGCGGACTTGGAGGTCGCCAACCGCCACGGCCACACCTGCCTCATGATTTCCTGCTACAAGGGC
CACAAAGAGATAGCCAAGTTTCTCCTGGACCGTGGGGCTGACGTGAACCGAAAGAGTGTGAAAGGGAACACGGCCCTCCA
TGACTGCGCTGAGTCTGGGAGTCTGGACATCATGAAGATGCTGCTGAAGTGCAACGCCCGCATGGAGAGGGACGGGTATG
GGATGACCCCACTCCTGGCTGCCAGTGTAACGGGGCACACTAACATTGTGGAGTATCTGGCCCACCAGCCTCGCACTTCC
AGAGAGGAGCGGATCAATGCACTGGAGCTACTGGGAGCAACGTTTGTGGACAAGAAACGTGATTTGTTGGGAGCGATGAG
GTACTGGAGAAGAGCTATTGAGCTGAGGGAGGCGGGGGACAAAGCTGGATCGCTGTCCAAGCCTCCGCCTGGTCCTCCCG
TCCCTGCCTACGGATGTGCCCAGGAGGTGAGCACTGCAGAGGAGCTTGAAGCTTTAATCACTGATCCTGATGAAATGAGG
ATGCAGGCCTTGCTGGTTCGTGAGCGCATCCTTGGGCCATCCCACCCGGACACATCTTATTACATTCGGTACAGGGGAGC
TGTGTATGCTGACTCGGGCAACTTTGAGCGCTGTATCAGTCTGTGGAAATATGCCTTAGACATGCAGCAGAGCAACTTGG
ACCCCCTCAGTCCCATGACAGCCTCCAGTTTCCTATCCTTCGCAGAGCTCTTTTCTTTTGTTCTTCAGGACAGGGCCAAA
GGCACCCTGTCAACTCGCATCACCTTCCAGGATCTAATGACTGTGCTGGGGAAAAGCGTGAGGGAAGTCGAAAGGGCTGT
GGCACAGAGAGACAACCCCCCAGATACCCCTCAGTTCAACAAGGCGCTTTCCATCATCCTCCACCTCATCTTTTTACTGG
AAAAGCTTGAGTGCAACCCCGAGCAGGAACACCAAAAGAAGCACACAGTCTACCGGCTGCTCAAGCTCAACCCTCGAGGT
CGGAACGGATTCACGCCGCTCCACATGGCCATGGACAAAGAGACCACATCTGTGGGCCGCTACCCAGTGGGCCGCTTCCC
CTCCCAGGCGGTGGCAGCGCTGCTCCTAGAGTGCGGCGCAGATGTCGATTCGCGGGACTGTGAGAACAACACCCCGCTGC
ACGTTGCCGCCAACAACGGTTGCCCAGAGATAATGGCGCTGCTGGTGAAGGCGGGGGCCCACTTCGACGCGACGAACGCT
CAGAGGAAAACAGCTTACGAACTGTTGGATGATCACAGCGGCGGCCACACGGCACTGTACCCGCTGAACTACATCACCCT
TCAGTGCCTGGCAGCTCGTGCGATTGAAAAGCACAGGCTGCCTTACAGGGGCCTGATCTCTGAGGAGATGGAGGCTTTCA
TTGAGCTCCACTGA

Alignment

ORF - retro_xmac_5 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 71.04 %
• Parental protein coverage: 99.84 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MDLKTAVYNAARDGKLRLLQKLLENKDGHEVTKLMGEKTNGATPLLMAARYGHLDLVEYLLECCCAPVEV
          MD...AV.NAARDGKL.L.QKLL.NK...E...L..EKT.G.T.LL.A.RYGHL..V.YLLE.C.A.VE.
Retrocopy MDITVAVFNAARDGKLKLIQKLLSNKTPEELEALAEEKTQGSTALLIASRYGHLEVVDYLLEHCKANVEL

Parental  GGSVNFDGETIEGAPPLWAASAAGHLKVVQSLLGHGASVNSTTLTNSTPLRAACFDGHLDIVRYLVEHKA
          GGSVNFDGETIEGAPPLWAASAAGHL.VV..LL.HGASVN..TLTNSTPLRAACFDGHL.IVRYLVEH.A
Retrocopy GGSVNFDGETIEGAPPLWAASAAGHLPVVKTLLKHGASVNNATLTNSTPLRAACFDGHLEIVRYLVEHRA

Parental  DLEVANRHGHTCLMISCYKGHKEIAQYLLEKGADVNRKSVKGNTALHDCAESGSLEIMRMLLQYGATMER
          DLEVANRHGHTCLMISCYKGHKEIA..LL..GADVNRKSVKGNTALHDCAESGSL.IM.MLL...A.MER
Retrocopy DLEVANRHGHTCLMISCYKGHKEIAKFLLDRGADVNRKSVKGNTALHDCAESGSLDIMKMLLKCNARMER

Parental  DGYGMTPLLSASVTGHTNIVDYLTTHQQTSHTERIDALELLGATFVDKKRDLLGALKYWKRAMDLRYT--
          DGYGMTPLL.ASVTGHTNIV.YL.....TS..ERI.ALELLGATFVDKKRDLLGA..YW.RA..LR....
Retrocopy DGYGMTPLLAASVTGHTNIVEYLAHQPRTSREERINALELLGATFVDKKRDLLGAMRYWRRAIELREAGD

Parental  DSNIVHKPEPKHLIMAYDYAKEVTNGEELDGLISDPDEMRMQALLIRERILGPQHPDTSYYIRYRGAVYA
          ......KP.P.....AY..A.EV...EEL..LI.DPDEMRMQALL.RERILGP.HPDTSYYIRYRGAVYA
Retrocopy KAGSLSKPPPGPPVPAYGCAQEVSTAEELEALITDPDEMRMQALLVRERILGPSHPDTSYYIRYRGAVYA

Parental  DSGNFERCINLWKYALEMQQNNLDPLSPMTTSSLLSFAELFSFMLQDRAKGLLGTSVSFEDLMGILTKSV
          DSGNFERCI.LWKYAL.MQQ.NLDPLSPMT.SS.LSFAELFSF.LQDRAKG.L.T...F.DLM..L.KSV
Retrocopy DSGNFERCISLWKYALDMQQSNLDPLSPMTASSFLSFAELFSFVLQDRAKGTLSTRITFQDLMTVLGKSV

Parental  LEIERAVKQIGPMPPDPAQLSKALSIILHLICLLEKVPCTTEQDHFKKETIYRFLKLQPCGKNGFTPLHL
          .E.ERAV.Q....PPD..Q..KALSIILHLI.LLEK..C..EQ.H.KK.T.YR.LKL.P.G.NGFTPLH.
Retrocopy REVERAVAQ-RDNPPDTPQFNKALSIILHLIFLLEKLECNPEQEHQKKHTVYRLLKLNPRGRNGFTPLHM

Parental  AVDRNTTCVGRYPVCKFPSLTVASILLECGADVNSRDEDDNSPLHIAASNGHPDIMNLLISCGNHFDSTN
          A.D..TT.VGRYPV..FPS..VA..LLECGADV.SRD...N.PLH.AA.NG.P.IM.LL...G.HFD.TN
Retrocopy AMDKETTSVGRYPVGRFPSQAVAALLLECGADVDSRDCENNTPLHVAANNGCPEIMALLVKAGAHFDATN

Parental  AFQQTACDLLDEKELARNVIQPINHTTLQCLAARAIIKHSLHYRGNIPEKLEAFVLLH
          A...TA..LLD..........P.N..TLQCLAARAI.KH.L.YRG.I.E..EAF..LH
Retrocopy AQRKTAYELLDDHSGGHTALYPLNYITLQCLAARAIEKHRLPYRGLISEEMEAFIELH

Legend:

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

Expression

RNA-Seq

Xiphophorus maculatus was not studied using RNA-Seq expression data.

ChIP-Seq

Xiphophorus maculatus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_xmac_5 retrocopy.

TSS

Xiphophorus maculatus was not studied using FANTOM5 data.

Lab

retro_xmac_5 was not experimentally validated.

Homology

Retrocopy orthology:

Xiphophorus maculatus does not belong to any of the species groups (eutheria, teleost or neognath), studied for retrocopy-based homology. For more information about studied groups, please go to help section.

---

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 ,