RetrogeneDB ID: retro_ttru_1812

Retrocopy location

• Organism: Dolphin (Tursiops truncatus)
• Coordinates: scaffold_92532:18146..19262(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSTTRG00000004689
• Aliases: None
• Description: None

Sequence

>retro_ttru_1812
TACCGCCAGGCCTCCCTGTATGTGGGTGACCTCCACGCGGATGTCACCGAGGACCTGCTGTTTAAGAAGTTCAGCGCTGT
GAGGCCCGTGCTGTCTATCCGCATCTGCAGGGACCTGGTCACCTGCCGCTCTCTGGGCTATGCCTACGTGAACTTTCTGC
AGCTGGCAGATGCCTAGAAGGCCCCGGACACCACGAACTTTGACCCTATAAAGGGCAAATCCATCCGTCTCATGTGGTCT
CAGCGTGACGCCTACTTGAGGAAATCTGGAATTGGGAACGTGTTCATCAAGAATCTGGACAAATCCATTGATAACAAAAC
CCTTTATGAACACTTTTCATCTTTTGGGAAGATCCTGTCCTCCAAGATGATGAGTGATGATCACAGCTCCAGGTGCTATG
CGTTCGTACACTTTCAGAACCAGATTGCCACCGACAGGGCCATCCAGGAGATGAATGGGGCACTGCTTAAGGACTGCAGG
CTGTTTGTTGGCAGATTCAAGAGCCGCAAAGATCGGGAAGCCGAGCTCCAAAACAAAGCCAGTGAGTTCACCAATGTTTA
CATCAAAAACTTCGGAGATGACATGGATGATGAGAGACTGAGGGAAGTTTTCAGCAAATATGGAAAAACCCTGAGTGTTA
AGGTGATGACAGATTCCAGTGGGAAATCCAAAGGCTTTGGCTTTGTGAGTTTTGATAGCCACGGGGCTGCCAAAAAGGCT
GTTGAAGAAATGAATGGAAAGGACATAAATGGACAACTGCTTTTTGTAGGCCGGGCACAAAAGAAAGCAGAGCGACAGGC
TGAGTTAAAGCAAATGTTTGAACAGCTGAAACAGGAAAGATTTCGGCAGTGCCGGGGAGCAAAGCTCTATATTAAGAACC
TGGATGAGACCATTGATGATGAAAAGCTACGGAGGGAATTTCTTCATTTGGATCATAGCAGAGTTAAGGTAATGCAAGAA
GAAGGGCGAAACAAAGGGTTTGGCTGATCTGCTTCTCCTCTCCTGAGGGAGCACTAAAGCAATGACTGAGATGAATGGCC
GCATCTTGGGCTCAAGCCGCTCAACATCGCCCTGGCCCAGAGGCTGTAGGAGAGGAAAACTTAATGCACCAGCCAG

Alignment

ORF - retro_ttru_1812 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 64.19 %
• Parental protein coverage: 60.32 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  YPMASLYVGDLHPDVTEAMLYEKFSPAGPILSIRVCRDMITRRSLGYAYVNFQQPADAERALDTMNFDVI
          Y..ASLYVGDLH.DVTE..L..KFS...P.LSIR.CRD..T.RSLGYAYVNF.Q.ADA..A.DT.NFD.I
Retrocopy YRQASLYVGDLHADVTEDLLFKKFSAVRPVLSIRICRDLVTCRSLGYAYVNFLQLADA*KAPDTTNFDPI

Parental  KGKPVRIMWSQRDPSLRKSGVGNIFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDENGSKGYGFVHFET
          KGK..R.MWSQRD..LRKSG.GN.FIKNLDKSIDNK.LY..FS.FG.ILS.K...D...S..Y.FVHF..
Retrocopy KGKSIRLMWSQRDAYLRKSGIGNVFIKNLDKSIDNKTLYEHFSSFGKILSSKMMSDDHSSRCYAFVHFQN

Parental  QEAAERAIEKMNGMLLNDRKVFAGRFKSRKEREAELGARAKEFTNVYIKNFGEDMDDERLKDLFGKFGPA
          Q.A..RAI..MNG.LL.D...F.GRFKSRK.REAEL...A.EFTNVYIKNFG.DMDDERL...F.K.G..
Retrocopy QIATDRAIQEMNGALLKDCRLFVGRFKSRKDREAELQNKASEFTNVYIKNFGDDMDDERLREVFSKYGKT

Parental  LSVKVMTDESGKSKGFGFVSFERHEDAQKAVDEMNGKELNGKQIYVGRAQKKVERQTELKRKFEQMKQDR
          LSVKVMTD.SGKSKGFGFVSF..H..A.KAV.EMNGK..NG....VGRAQKK.ERQ.ELK..FEQ.KQ.R
Retrocopy LSVKVMTDSSGKSKGFGFVSFDSHGAAKKAVEEMNGKDINGQLLFVGRAQKKAERQAELKQMFEQLKQER

Parental  ITRYQGVNLYVKNLDDGIDDERLRKEFSPFGTITSAKVMMEGGRSKGFG-FVCFSSPEEA-TKAVTEMNG
          .....G..LY.KNLD..IDDE.LR.EF.............EG.R.KGFG...CFSSPE.A.TKA.TEMNG
Retrocopy FRQCRGAKLYIKNLDETIDDEKLRREFLHLDHSRVKVMQEEG-RNKGFG<LICFSSPEGA<TKAMTEMNG

Parental  RIVAT-KPLYVALAQRKEERQAHLTNQ
          RI....KPL..ALAQR..ER....T.Q
Retrocopy RILGS<KPLNIALAQRL*ERKT*CTSQ

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_1812 retrocopy.

TSS

Tursiops truncatus was not studied using FANTOM5 data.

Lab

retro_ttru_1812 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.

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Parental genes homology:

Parental genes homology involve 16 parental genes, and 38 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000015833	5 retrocopies	retro_cjac_1586, retro_cjac_2571, retro_cjac_3218, retro_cjac_4039, retro_cjac_41,
Homo sapiens	ENSG00000070756	1 retrocopy	retro_hsap_88,
Macaca mulatta	ENSMMUG00000017786	2 retrocopies	retro_mmul_1462, retro_mmul_895,
Monodelphis domestica	ENSMODG00000006222	4 retrocopies	retro_mdom_123, retro_mdom_1867, retro_mdom_216, retro_mdom_43,
Mus musculus	ENSMUSG00000022283	2 retrocopies	retro_mmus_102, retro_mmus_2164,
Nomascus leucogenys	ENSNLEG00000003142	3 retrocopies	retro_nleu_221, retro_nleu_2412, retro_nleu_611,
Oryctolagus cuniculus	ENSOCUG00000004354	1 retrocopy	retro_ocun_13,
Pongo abelii	ENSPPYG00000018790	3 retrocopies	retro_pabe_2373, retro_pabe_68, retro_pabe_854,
Pteropus vampyrus	ENSPVAG00000016640	2 retrocopies	retro_pvam_10, retro_pvam_855,
Rattus norvegicus	ENSRNOG00000008639	3 retrocopies	retro_rnor_1228, retro_rnor_2321, retro_rnor_265,
Sarcophilus harrisii	ENSSHAG00000011267	1 retrocopy	retro_shar_24,
Sus scrofa	ENSSSCG00000006063	2 retrocopies	retro_sscr_1153, retro_sscr_1205,
Tursiops truncatus	ENSTTRG00000002117	1 retrocopy	retro_ttru_715,
Tursiops truncatus	ENSTTRG00000004689	2 retrocopies	retro_ttru_1050, retro_ttru_1812 ,
Tursiops truncatus	ENSTTRG00000014340	2 retrocopies	retro_ttru_1117, retro_ttru_246,
Vicugna pacos	ENSVPAG00000003865	4 retrocopies	retro_vpac_14, retro_vpac_384, retro_vpac_620, retro_vpac_649,