RetrogeneDB ID: retro_ttru_951

Retrocopy location

• Organism: Dolphin (Tursiops truncatus)
• Coordinates: GeneScaffold_777:164515..165641(-)
• Located in intron of: ENSTTRG00000001153

Retrocopy information

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

Parental gene information

• Parental gene symbol: HSPD1
• Ensembl ID: ENSTTRG00000003417
• Aliases: None
• Description: heat shock 60kDa protein 1 (chaperonin) [Source:HGNC Symbol;Acc:5261]

Sequence

>retro_ttru_951
CAAGAGGGTGGGGATGGTACCACTACTGCTACTGTACTGGCTCTATCGCCAAGGAAGGCTTCGAGAAGCTTAGCAAAGGT
GCTAATCCAGTGGAAATCAGGGGAGGTGTGATGTTAGCTGTTGATGCTATAATTGCTGAACTTAAGAAGCAGTCTAAACC
TGTGGCAACCCCAGAAGAGATAGCCCAGGTTACTACGATTCCTGCCAATGGAGACAAAGAAATTGGCAACGTCATTTCTG
ATGCGATGAAAAAGGTTGGAAGAAAGTGCGTTATCACAGTAAAGGATGGAAAAACACTGAATGACGAAATTAGAAATTAT
TGAAGGCATGAAGTTTGTTAGAGGGTATATCTCTGCATACTTTATTAATACATCAAAAGGTCAGAAATGTGAATTCCAAG
ATGCGTATGTTCTGTTGAGTGAAAAGAAAATTTTGGTGTCCAGTCCATTGTTCCTGCTCTTGAAATTGCCAACGCTCACC
ATAAGCCCTTGGTCATAATTGCTGAAGATGTGGATGGAGAAGCTCTAAGTACACTTGTTTTGAATAGGCTGAAAGTTGGT
CTTCAGGTTGTAGCAGTCAAAGGTCCAGGTTTTGGTGACAATAGAAAGAACCAGCTTAAAGACATGGCTATTGCTACTGG
TGGTACAGTATTTGGAGAAGAAGGGCTAACTCTAAATCTTGAAAATGTTCAGCCTCATGACTTAGGAAAAGTTGGAGAGA
TCATTGTGACCAAAGATGATGCCATGCTCTTGAAAGGAAAAGGTGACAAGGCTCAAATTGAAAAGCGTATTCAAGAAATC
ATCGAGCAGTTAGATATTACATCTAGTGAATATGAAAAGGAAAAACTGAATGAACGTCTGGCAAAACTCTCAGATGGTGT
TGCTGTGCTAAAGGTTGGTGGGACAAGTGACGTTGAAGTGAATGGAAAGAAAGACAGAGTTACAGATGCCCTTAATGCTA
TGTGAGCTGCTGTTGAAGAACGCATTGTTTTGGGAAGGGGCTGTGCCCTGCTTCAGTGCCTTCCAGCCTTGGATTCAAAA
CTCCAGCTAATGAAGATCAAAAAATTAGTATAGAAATTATTTTTAAAACACTCAAAATTCCTGCAGTGACCATTGCTAAG
AATGCA

Alignment

ORF - retro_ttru_951 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 88.71 %
• Parental protein coverage: 65.79 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  EEAGDGTTTATVLAR-SIAKEGFEKISKGANPVEIRRGVMLAVDAVIAELKKQSKPVTTPEEIAQVATIS
          .E.GDG.TT.......SIAKEGFEK.SKGANPVEIR.GVMLAVDA.IAELKKQSKPV.TPEEIAQV.TI.
Retrocopy QEGGDG-TTTATVLA<SIAKEGFEKLSKGANPVEIRGGVMLAVDAIIAELKKQSKPVATPEEIAQVTTIP

Parental  ANGDKEIGSIISDAMKKVGRKGVITVKDGKTLNDE-LEIIEGMKFDRGYISPYFINTSKGQKCEFQDAYV
          ANGDKEIG..ISDAMKKVGRK.VITVKDGKTLNDE.LEIIEGMKF.RGYIS.YFINTSKGQKCEFQDAYV
Retrocopy ANGDKEIGNVISDAMKKVGRKCVITVKDGKTLNDE>LEIIEGMKFVRGYISAYFINTSKGQKCEFQDAYV

Parental  LLSEKKIS-SVQSIVPALEIANAHRKPLVIIAEDVDGEALSTLVLNRLKVGLQVVAVKAPGFGDNRKNQL
          LLSEKKI...VQSIVPALEIANAH.KPLVIIAEDVDGEALSTLVLNRLKVGLQVVAVK.PGFGDNRKNQL
Retrocopy LLSEKKIL<GVQSIVPALEIANAHHKPLVIIAEDVDGEALSTLVLNRLKVGLQVVAVKGPGFGDNRKNQL

Parental  KDMAIATGGAVFGEEGLTLNLEDVQPHDLGKVGEVIVTKDDAMLLKGKGDKAQIEKRIQEIIEQLDITTS
          KDMAIATGG.VFGEEGLTLNLE.VQPHDLGKVGE.IVTKDDAMLLKGKGDKAQIEKRIQEIIEQLDIT.S
Retrocopy KDMAIATGGTVFGEEGLTLNLENVQPHDLGKVGEIIVTKDDAMLLKGKGDKAQIEKRIQEIIEQLDITSS

Parental  EYEKEKLNERLAKLSDGVAVLKVGGTSDVEVNEKKDRVTDALNATRAAVEEGIVLGGGCALLRCLPALDS
          EYEKEKLNERLAKLSDGVAVLKVGGTSDVEVN.KKDRVTDALNA..AAVEE.IVLG.GCALL.CLPALDS
Retrocopy EYEKEKLNERLAKLSDGVAVLKVGGTSDVEVNGKKDRVTDALNAM*AAVEERIVLGRGCALLQCLPALDS

Parental  -ITPANEDQKIGIEIIKKALKIPAMTIAKNA
          ..TPANEDQKI.IEII.K.LKIPA.TIAKNA
Retrocopy <KTPANEDQKISIEIIFKTLKIPAVTIAKNA

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_951 retrocopy.

TSS

Tursiops truncatus was not studied using FANTOM5 data.

Lab

retro_ttru_951 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 51 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000013770	1 retrocopy	retro_amel_771,
Bos taurus	ENSBTAG00000012586	1 retrocopy	retro_btau_988,
Canis familiaris	ENSCAFG00000010865	4 retrocopies	retro_cfam_1185, retro_cfam_1620, retro_cfam_2165, retro_cfam_614,
Callithrix jacchus	ENSCJAG00000003990	6 retrocopies	retro_cjac_1516, retro_cjac_1534, retro_cjac_1975, retro_cjac_3172, retro_cjac_3400, retro_cjac_4096,
Dasypus novemcinctus	ENSDNOG00000013226	3 retrocopies	retro_dnov_1990, retro_dnov_2113, retro_dnov_2512,
Echinops telfairi	ENSETEG00000009184	4 retrocopies	retro_etel_1440, retro_etel_426, retro_etel_885, retro_etel_925,
Loxodonta africana	ENSLAFG00000000053	1 retrocopy	retro_lafr_476,
Macropus eugenii	ENSMEUG00000011987	2 retrocopies	retro_meug_1688, retro_meug_224,
Myotis lucifugus	ENSMLUG00000000871	4 retrocopies	retro_mluc_1458, retro_mluc_2280, retro_mluc_2348, retro_mluc_601,
Macaca mulatta	ENSMMUG00000010489	1 retrocopy	retro_mmul_83,
Monodelphis domestica	ENSMODG00000012289	3 retrocopies	retro_mdom_427, retro_mdom_493, retro_mdom_756,
Mustela putorius furo	ENSMPUG00000007818	3 retrocopies	retro_mputfur_1118, retro_mputfur_245, retro_mputfur_434,
Otolemur garnettii	ENSOGAG00000034053	5 retrocopies	retro_ogar_2335, retro_ogar_2420, retro_ogar_2740, retro_ogar_3221, retro_ogar_3497,
Rattus norvegicus	ENSRNOG00000014525	9 retrocopies	retro_rnor_1000, retro_rnor_1006, retro_rnor_1308, retro_rnor_1578, retro_rnor_1585, retro_rnor_2812, retro_rnor_2835, retro_rnor_596, retro_rnor_905,
Tursiops truncatus	ENSTTRG00000003417	3 retrocopies	retro_ttru_1661, retro_ttru_1798, retro_ttru_951 ,
Xenopus tropicalis	ENSXETG00000007509	1 retrocopy	retro_xtro_63,