RetrogeneDB ID: retro_ttru_1648

Retrocopy location

• Organism: Dolphin (Tursiops truncatus)
• Coordinates: scaffold_83058:48557..49843(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: None
• Aliases: None
• Status: NOVEL

Parental gene information

• Parental gene symbol: GMCL1
• Ensembl ID: ENSTTRG00000007493
• Aliases: None
• Description: germ cell-less, spermatogenesis associated 1 [Source:HGNC Symbol;Acc:23843]

Sequence

>retro_ttru_1648
CTCACAAAAGCGCCCCACCAGAAACATGCTAAAGATTGTTCAGGGTCCATTTATGAGGCACTCTTCCTGAGAGGAGAAGA
GAGTGACGTGAGGATCCACGCACTGGGGGAGGAGTGGAACTTGCGTTGGGTCTACTTGAGCCAGTCAGGGTACTTTGTTA
GCAGTTCAGTGGTGCTTGGTAGGAGACAACCATGGATACTATAGAGTTGCAGATGCCTGATGAGAATATTGATCGTGAGG
CACTGCACGAGGCTTTAGGTTCCCTGTACCGAGACTCCATGCTCATCCAACCCGGTCGAGTCGCTGCCATCCTGGCCACA
GCCAGCATGCTGCAACTGGACGAGCTGATTCAGCAGTGCGGGAAAGTCATGAAGGAGACTGTCAGTGCCCAGACGGTGTG
CAGCTACTACGACTCTGCTGAAAGTTACAGACTCCAGAACATCAGGACCATGTGTCTTCAGTGGCTACTGGACAACATGA
CGACCCAGTGTAGTGAGGAGTTATTGCAAGAAGTCAGCCTGGATCTCATGAAAGAGGTCATTGCCTCTTCAGAGCTCTTG
ATGATGTAGGTGGAGATGGACGTGTAAACCATGCTGAAAAAGTGGATGTTCTTGTAGCTGCAGCCGACATGGAGGGGCCC
ACGCAGGGCCCTATTGCCTGACAATGACTCGTGGTTTGCCAGGTCCAGGAGGGAGTCGGAGGGCACCATTTTCCTGGGGA
CCGAGCAGGACAGAGCCTTCTTGCTAGTGTTCCAGCAGCTGTGGCTTGCCTACATAATCTGGGACCTGACGTCAGCACAT
GTCATCCACCAGGATGCGATGATCCCTGCTGCTTGGCTGTCTCCAGTGTACAAAGAGCATTGGCTTGGCCCCCTCCGGGC
TGAGCAGACCAGAAAGCTCTGGCCCGTGGACATCTGCGTGTCTGACCCCCAGGGGAAGAGCATGTGGTGTGGGGGCCAGC
TTCACAGGGACAAGCAGTGCAGCTGGCAGTGGGAAGGCTTCAACTTCAGCTGGGACCTGGTAGTGTGCTACGTCAACCAG
CACATCATTTTCTGGTGCAGTGCAGTGAACAAGTCCTGCAGCCTCGGGATCAGCTTACTCTGGCAGAGAAAGTTCGCCTT
CTACCTGTGCCTGTTCTCCTTGGACAAGGCTGGGAGATTCGTTTTCAGGAAGGACACAAAATACCTGATGTTTTCCCTGA
GAAAGGGTCAAGTGCTAGACATAGTGAACCTGGAAAACCAAGACGTGGTTTTCCCCATATATGTAGCCTGTAACTTCTTG
TACCTC

Alignment

ORF - retro_ttru_1648 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 50.47 %
• Parental protein coverage: 83.63 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  LLNTPRRKKLKSTSKYIYQTLFLNGENSDIKICALGEEWSLHKIYLCQSGYFSS-MFSGSWKESSMNIIE
          L...P..K..K..S..IY..LFL.GE.SD..I.ALGEEW.L...YL.QSGYF.S..FSG.W.E..M..IE
Retrocopy LTKAPHQKHAKDCSGSIYEALFLRGEESDVRIHALGEEWNLRWVYLSQSGYFVS<QFSGAW*ETTMDTIE

Parental  LEIPDQNIDIEALQVAFGSLYRDDVLIKPSRVIAILAAASMLQLDGLIQQCGETMKETVNVKTVCGYYTS
          L..PD.NID.EAL..A.GSLYRD..LI.P.RV.AILA.ASMLQLD.LIQQCG..MKETV...TVC.YY.S
Retrocopy LQMPDENIDREALHEALGSLYRDSMLIQPGRVAAILATASMLQLDELIQQCGKVMKETVSAQTVCSYYDS

Parental  AGTYGLDSVKKKCLEWLLNNLMTHQNVELFKELSINVMKQLIGSSNLFVMQVEMDVYTALKKWMFLQLVP
          A..Y.L......CL.WLL.N..T....EL..E.S...MK..I.SS.L..M.VEMDV.T.LKKWMFL.L.P
Retrocopy AESYRLQNIRTMCLQWLLDNMTTQCSEELLQEVSLDLMKEVIASSELLMM*VEMDV*TMLKKWMFL*LQP

Parental  SWNGSLKQLLTETDVWFSNRRKDFEGMTFLETEQGKPFMSVFRHLRLQYIISDLASARIIEQDSLVPSEW
          .W.G....LL...D.WF...R...EG..FL.TEQ...F..VF..L.L.YII.DL.SA..I.QD...P..W
Retrocopy TWRGPRRALLPDNDSWFARSRRESEGTIFLGTEQDRAFLLVFQQLWLAYIIWDLTSAHVIHQDAMIPAAW

Parental  LSSVYKQQWFAMLRAEQDSEVGPQEINKEELEGNSMRCGRKLAKDGEYCWRWTGFNFGFDLLVTYTNRYI
          LS.VYK..W...LRAEQ.....P..I......G.SM.CG..L..D....W.W.GFNF..DL.V.Y.N..I
Retrocopy LSPVYKEHWLGPLRAEQTRKLWPVDICVSDPQGKSMWCGGQLHRDKQCSWQWEGFNFSWDLVVCYVNQHI

Parental  IFKRNTLNQPCSGSVSLQPRRSIAFRLRLASFDSSGKLICSRTTGYQILTLEKDQEQVVMNLDSRLLIFP
          IF.....N..CS...SL...R..AF.L.L.S.D..G.......T.Y....L.K.Q.....NL......FP
Retrocopy IFWCSAVNKSCSLGISLLWQRKFAFYLCLFSLDKAGRFVFRKDTKYLMFSLRKGQVLDIVNLENQDVVFP

Parental  LYICCNFLYI
          .Y..CNFLY.
Retrocopy IYVACNFLYL

Legend:

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

Expression

RNA-Seq

Tursiops truncatus was not studied using RNA-Seq expression data.

ChIP-Seq

Tursiops truncatus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ttru_1648 retrocopy.

TSS

Tursiops truncatus was not studied using FANTOM5 data.

Lab

retro_ttru_1648 was not experimentally validated.

Homology

Retrocopy orthology:

Tursiops truncatus 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 19 parental genes, and 29 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000016116	1 retrocopy	retro_amel_1915,
Choloepus hoffmanni	ENSCHOG00000012306	2 retrocopies	retro_chof_1562, retro_chof_802,
Equus caballus	ENSECAG00000016813	2 retrocopies	retro_ecab_1109, retro_ecab_899,
Homo sapiens	ENSG00000087338	1 retrocopy	retro_hsap_3407,
Loxodonta africana	ENSLAFG00000002565	3 retrocopies	retro_lafr_220, retro_lafr_592, retro_lafr_98,
Myotis lucifugus	ENSMLUG00000009183	2 retrocopies	retro_mluc_1521, retro_mluc_31,
Macaca mulatta	ENSMMUG00000000858	1 retrocopy	retro_mmul_98,
Mus musculus	ENSMUSG00000001157	1 retrocopy	retro_mmus_3665,
Nomascus leucogenys	ENSNLEG00000010132	1 retrocopy	retro_nleu_2993,
Oryctolagus cuniculus	ENSOCUG00000015808	2 retrocopies	retro_ocun_112, retro_ocun_160,
Otolemur garnettii	ENSOGAG00000008408	1 retrocopy	retro_ogar_151,
Pongo abelii	ENSPPYG00000012334	1 retrocopy	retro_pabe_209,
Pan troglodytes	ENSPTRG00000012021	1 retrocopy	retro_ptro_2314,
Pteropus vampyrus	ENSPVAG00000001242	3 retrocopies	retro_pvam_1259, retro_pvam_370, retro_pvam_816,
Sorex araneus	ENSSARG00000004651	1 retrocopy	retro_sara_425,
Sus scrofa	ENSSSCG00000008335	1 retrocopy	retro_sscr_62,
Ictidomys tridecemlineatus	ENSSTOG00000000714	1 retrocopy	retro_itri_59,
Tursiops truncatus	ENSTTRG00000007493	3 retrocopies	retro_ttru_1039, retro_ttru_1647, retro_ttru_1648 ,
Vicugna pacos	ENSVPAG00000001756	1 retrocopy	retro_vpac_617,