RetrogeneDB ID: retro_gmor_12

Retrocopy location

• Organism: Cod (Gadus morhua)
• Coordinates: GeneScaffold_3230:17070..18927(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSGMOG00000019730
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: fem1c
• Ensembl ID: ENSGMOG00000005806
• Aliases: None
• Description: fem-1 homolog c (C.elegans) [Source:ZFIN;Acc:ZDB-GENE-031008-3]

Sequence

>retro_gmor_12
ATGGATTTAACGACGACCGTGTTCAACGCGGCCAGATATGGTAAGCTGAAACTTATACAGAAGTTGCTGAGCAACAAAAC
TCCAGAGGAGCTGGAGGCTCTAGCTGAGGAGAAAACCCAGGGGGGAACCCCTCTGTTGATCGCCTCTCGATACGGACATT
TAGAAGTGGTGGGATACCTCCTAGAACAATGTAAGGCTAATGTTGAACTGGGAGGGTCTGTCAATTTTGACGGCGAGACC
ATCGAGGGAGCGCCGCCGCTGTGGGCGGCCTCTGCCGCCGGCCACCTCCCTGTGGTCAGGGCGCTGCTGAGGCGCGGTGC
CTCGGTCAACAACGCAACGCTGACCAACTCGACCCCACTACGAGCCGCCTGTTTCGACGGTCACCTCGAGATCGTCCGGT
ACTTGGTGGAACACAGCGCTGACATGGAGGTGGCCAACCGCCACGGCCACACATGCCTTATGATATCGTGCTATAAGGGT
CACAAAGATATAGCCAAGTTCCTCCTAGATCGCGGTGCTGACGTCAACCGCAAAAGCGTCAAAGGCAACACTGCCCTCCA
CGACTGTGCCGAATCAGGAAGTTTGGACATCATGAAGATGCTGTTGAAATGTAATGCGCGCATGGAAAGAGATGGATACG
GAATGACACCGCTGCTGGCTGCCAGTGTGACGGGTCACACTAACATCGTTGAGTACCTCGCCCATCAACCTCGCTCTGTA
AGGGAAGAACGAATCGATGCACTTGAACTGCTTGGGGCCACTTTTGTAGACAAAAAACGAGATCTCCTCGGAGCAATGAG
ATACTGGAGGCGGGCCATGGAGTTAAGGCAACCCGGAGACAAAACAGCTTTATTAGCCAAACCCCTGCCCAGACCTCCAA
TCTCTGCGTACAACTGTGCCCAGGAAGTGACCACTGCGGACGAGCTGGAGGCTCTTATAACAGACCCGGATGAGATGCGG
ATGCAGGCCTTACTGGTCCGTGAGCGCATTCTGGGCCCGTCTCACCCCGACACCTCTTACTACATCCGCTACAGAGGAGC
CGTCTACGCCGACTCGGGAAACTTTGAGCGCTGCATCAGCCTGTGGAAGTACGCCCTTGACATGCAGCAGAGCAACCTGG
ACCCCCTCAGTCCCATGACGGCTTCCAGCTTCTTATCCTTCGCAGAGCTCTTCTCCTTCGTCCTCCAGGACCGCGCCAAG
GGCACCCTGGCGACGCGCATCACCTTCCACGACCTGATGTGCGTCCTGGGCAAGAGCGTGCGGGAGGTGGAGCGGGCGGT
GGCCCTGAGGGACCACCCGCCGGAGGCGCCGCAGTTCACCAAGGCGCTGTCCATCATCCTGCACCTGGTCTTCCTGCTGG
AGAAGCTGGAGTGCACGGCGGAGCAGGAGCACCAGAAGAAGCAGACGGTGTATCGGCTGCTGAAGCTCAACCCGCGCGGC
CGCGGCGGCTCCACGCCCCTGCACATGGCCGTGGACAAGGACACCACGTCCGTGGGCCGCTACCCCGTGGGCCGCTTCCC
CTCGCAGGCCGTCGCCTCGCTGCTGCTGGAGTGCGGGGCCGACATCGACTCGCGAGACCTGGACAACAACACACCGCTGC
ACGTGGCCGCCGCCAACGGCTGCCCCAAGATCATGGCACTGCTCGTGAGCGCCGGGGCGCACTTTGACGCCACGAACGCA
AAGCGGAAGGCGGCCTACGAGTTGCTGGAGGAGCAGAGCAGCCCTGGCCACCCGGCGATCTGCCCCTTGAACTACATCAC
CCTCCAGTGCCTGGCAGCGCGGGCGGTGGAGAGGCACAGACTGCCCTACAAGGGGCTTATCTCGGAGGAGATGGAGGCTT
TCATTGAGCTGCACTGA

Alignment

ORF - retro_gmor_12 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 70.44 %
• Parental protein coverage: 99.84 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MDLKTAVFNAARDGKLRLLQKLLENKDGHEVTKLMGEKTNGATPLLMASRYGHLDLVEYLIECCSAAVEV
          MDL.T.VFNAAR.GKL.L.QKLL.NK...E...L..EKT.G.TPLL.ASRYGHL..V.YL.E.C.A.VE.
Retrocopy MDLTTTVFNAARYGKLKLIQKLLSNKTPEELEALAEEKTQGGTPLLIASRYGHLEVVGYLLEQCKANVEL

Parental  GGSVNFDGETIEGAPPLWAASAAGHLKVVQSLLGHGASVNNTTLTNSTPLRAACFDGHLDIVKYLVEHKA
          GGSVNFDGETIEGAPPLWAASAAGHL.VV..LL..GASVNN.TLTNSTPLRAACFDGHL.IV.YLVEH.A
Retrocopy GGSVNFDGETIEGAPPLWAASAAGHLPVVRALLRRGASVNNATLTNSTPLRAACFDGHLEIVRYLVEHSA

Parental  DLEVANRHGHTCLMISCYKGHKEIAQYLLEKGADVNRKSVKGNTALHDCAESGSLEIMRMLLQYGASMER
          D.EVANRHGHTCLMISCYKGHK.IA..LL..GADVNRKSVKGNTALHDCAESGSL.IM.MLL...A.MER
Retrocopy DMEVANRHGHTCLMISCYKGHKDIAKFLLDRGADVNRKSVKGNTALHDCAESGSLDIMKMLLKCNARMER

Parental  DGYGMTPLLSASVTGHTNIVDFLTTHQKTSHRERIDALELLGATFVDKKRDLLGALKYWKRAMDLRYI-D
          DGYGMTPLL.ASVTGHTNIV..L.........ERIDALELLGATFVDKKRDLLGA..YW.RAM.LR...D
Retrocopy DGYGMTPLLAASVTGHTNIVEYLAHQPRSVREERIDALELLGATFVDKKRDLLGAMRYWRRAMELRQPGD

Parental  SNNIVQKPEPKHLIMAYDYAKEVTNGEELDGLISDPDEMRMQALLIRERILGPQHPDTSYYIRYRGAVYA
          ......KP.P...I.AY..A.EVT...EL..LI.DPDEMRMQALL.RERILGP.HPDTSYYIRYRGAVYA
Retrocopy KTALLAKPLPRPPISAYNCAQEVTTADELEALITDPDEMRMQALLVRERILGPSHPDTSYYIRYRGAVYA

Parental  DSGNFERCINLWKYALDMQQSNLDPLSPMTASSLLSFAELFSFMLQDRAKGVLGTSVSFEDLMGILTKSV
          DSGNFERCI.LWKYALDMQQSNLDPLSPMTASS.LSFAELFSF.LQDRAKG.L.T...F.DLM..L.KSV
Retrocopy DSGNFERCISLWKYALDMQQSNLDPLSPMTASSFLSFAELFSFVLQDRAKGTLATRITFHDLMCVLGKSV

Parental  LEIERAVKQVGPTPPDPAQLSKALSIILHLICLLEKVPCTAEQDHFKKQTIYRFLKLQPCGKNGYSPLHL
          .E.ERAV......PP...Q..KALSIILHL..LLEK..CTAEQ.H.KKQT.YR.LKL.P.G..G..PLH.
Retrocopy REVERAV-ALRDHPPEAPQFTKALSIILHLVFLLEKLECTAEQEHQKKQTVYRLLKLNPRGRGGSTPLHM

Parental  AVDRNTTCVGRYPVCKFPSLTVASILLECGADVNCRDEDDNSPLHVAASNGHPDIMNLLISGGSHFDSTN
          AVD..TT.VGRYPV..FPS..VAS.LLECGAD...RD.D.N.PLHVAA.NG.P.IM.LL.S.G.HFD.TN
Retrocopy AVDKDTTSVGRYPVGRFPSQAVASLLLECGADIDSRDLDNNTPLHVAAANGCPKIMALLVSAGAHFDATN

Parental  AFQQSACDLLDKKEL-ARNIIQPINHTTLQCLAARVIVKHSLHYRGNIPEKLESFVLLH
          A....A..LL..........I.P.N..TLQCLAAR....H.L.Y.G.I.E..E.F..LH
Retrocopy AKRKAAYELLEEQSSPGHPAICPLNYITLQCLAARAVERHRLPYKGLISEEMEAFIELH

Legend:

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

Expression

RNA-Seq

Gadus morhua was not studied using RNA-Seq expression data.

ChIP-Seq

Gadus morhua was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_gmor_12 retrocopy.

TSS

Gadus morhua was not studied using FANTOM5 data.

Lab

retro_gmor_12 was not experimentally validated.

Homology

Retrocopy orthology:

Gadus morhua 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.

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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,