RetrogeneDB ID: retro_ttru_1213

Retrocopy location

• Organism: Dolphin (Tursiops truncatus)
• Coordinates: scaffold_107342:11332..12341(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: TRAF7
• Ensembl ID: ENSTTRG00000008169
• Aliases: None
• Description: TNF receptor-associated factor 7, E3 ubiquitin protein ligase [Source:HGNC Symbol;Acc:20456]

Sequence

>retro_ttru_1213
GACTCCTCCATCTCCATCTGCTTCCTCCACTCTGAGCCCAGCGTGTCCCTGTTCCCCACGTTCTCCCTGTCCTATGGGGA
GAAGGAGCCAAAGACACCGGGGTTTGCCTAGCAGCCCTCAGAAAGCTCTGCTTCCAGCTTTGCTGCCGTTTGTTCAAGGA
CCTTGAGATCACCATGTGTATACACACATTCTGTCAAAGATGCTCCTTGAAGTCACAGAAGGGTCCTGTGGACAATGCCA
AGCTGACGGTGGTAGAGAACACCAGTGCGGTGGCTGAGCAGATCTGGGAGCTCTTCATTCACTGAAAGCCTGTCTGCAAC
ATGGCAGGGATCAGAAGCCATCTTCTTGGATGTGTACCTCCATGGTGCCTTTCACCATCAAGTTTAGTGCTTAGAAGAAC
CAAAAGGGGAGCTGTGACTACAGCCCCAATGTGCCCCCAACAACCCCAGCTACTGCTCTTCCTCAAGATGAACCTGGAGG
CTCATCTCAAAGAGTGTGAACACATCAAGTATCCTCATTCCAAGTACTGACACATGTTCAATGGGAACCAGGACATGTAT
GAGACACACCTGGGGACATGCCACTTCAAGAGCTTACATGGATTCCTGCAGTCAAGGGACAAATGCTTCCATGAGGTACA
CGTAGTGCTGGCCTGGAAGAACCAGGAAAATCACTCTCTTTCTTCTATGCTGGGCAAAGTCTCAGAGAATACTGACAAGC
TGATGAAGAGCCTTGAGCTCAAGTTTGATGTCATGGACAAAAAATAGAGCCAGCTCAGCTACGACCTCATGGAGTTCCAG
AGGGAGGTATCTAATGTTGAATGACGAGCTGTCCCACACCAGTGCATGGCTGAACACGGGCATCCTAGGATCCTAAGACC
CTCAGCAGATTTTCAACTTCAAAGGAAACTTTCTGGTCCATCAGTGCCCCATCTGCTGTCTCTGTTCTATTCCATGGATG
ACCTGCCCTTAGGGGCTCCTCTGACCAGACCACCAATACATGGGACACA

Alignment

ORF - retro_ttru_1213 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 60.29 %
• Parental protein coverage: 50.6 %
• Number of stop codons detected: 5
• Number of frameshifts detected: 6

Retrocopy - Parental Gene Alignment:

Parental  DSAISVRSLHSESSMSLRSTFSLPEEEEEPEPLVFAEQPSV-KLCCQLCCSVFKDPVITTCGHTFCRRCA
          DS.IS...LHSE.S.SL..TFSL...E.EP....FA.QPS..KLC.QLCC..FKD..IT.C.HTFC.RC.
Retrocopy DSSISICFLHSEPSVSLFPTFSLSYGEKEPKTPGFA*QPSE<KLCFQLCCRLFKDLEITMCIHTFCQRCS

Parental  LKSEKCPVDNAKLTVVVNNIAVAEQIGELFIHCRHGCRAVGGGKPTVFEVDPRGC-PFTIKLSA-RKDHE
          LKS.K.PVDNAKLTVV.N..AVAEQI.ELFIH....C....G.........P..C.PFTIK.SA.R....
Retrocopy LKSQKGPVDNAKLTVVENTSAVAEQIWELFIH*KPVCN-MAGIRSHLLGCVPPWC<PFTIKFSA>RRTKR

Parental  GSCDYRPVRCPNNPSCPPLLKMNLEAHLKECEHIKCPHSKYGCTFIGNQDTYETHLETCRFEGLKEFLQQ
          G.....P..CP..P.....LKMNLEAHLKECEHIK.PHSKY...F.GNQD.YETHL.TC.F..L..FLQ.
Retrocopy GAVTTAPM-CPQQPQLLLFLKMNLEAHLKECEHIKYPHSKY*HMFNGNQDMYETHLGTCHFKSLHGFLQS

Parental  TDDRFHEMHVALAQKDQEIAFLRSMLGKLSEKIDQLEKSLELKFDVLDENQSKLSEDLMEFRRDAS-MLN
          .D..FHE.HV.LA.K.QE...L.SMLGK.SE..D.L.KSLELKFDV.D...S.LS.DLMEF.R..S.MLN
Retrocopy RDKCFHEVHVVLAWKNQENHSLSSMLGKVSENTDKLMKSLELKFDVMDKK*SQLSYDLMEFQREVS>MLN

Parental  DELSHINARLNMGILGSYDPQQIFKCKGTFVGHQGPVWCLC-VYSMGDL-LFSGSSDKTIKVWDT
          DELSH..A.LN.GILGS.DPQQIF..KG.F..HQ.P..CLC..YSM.DL....GSSD.T...WDT
Retrocopy DELSHTSAWLNTGILGS*DPQQIFNFKGNFLVHQCPICCLC<FYSMDDL<ALRGSSDQTTNTWDT

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_1213 retrocopy.

TSS

Tursiops truncatus was not studied using FANTOM5 data.

Lab

retro_ttru_1213 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 2 parental genes, and 2 retrocopies.

Species	Parental gene accession	Retrocopies number
Ictidomys tridecemlineatus	ENSSTOG00000013083	1 retrocopy	retro_itri_1441,
Tursiops truncatus	ENSTTRG00000008169	1 retrocopy	retro_ttru_1213 ,