RetrogeneDB ID: retro_ttru_1120

Retrocopy location

• Organism: Dolphin (Tursiops truncatus)
• Coordinates: scaffold_104105:38316..39119(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: NT5DC2
• Ensembl ID: ENSTTRG00000008562
• Aliases: None
• Description: 5'-nucleotidase domain containing 2 [Source:HGNC Symbol;Acc:25717]

Sequence

>retro_ttru_1120
CTGAACCTGGCAGCTGTCTATGCCAGTAATGAGATGAACATGAGTGATGTCAGGGTCTATAGCTCTCACTATGAAGAGAT
GCTGGCCCAGAACACAGCTGCATTGCACCTAGCGATCTACAGTGCTGCACATGACATCCTGATTGAGCAGTACAAATGCT
CAGAAGGGATTCAGAAGTATGACTACAACCTCTAGTTTGCCTTTGGGGACTCCACTATGACATTCAGAAGAGTATTCAGA
TGAAGAATGATGCCTTCCATTATATGCAACTGGGGAATGCCTCGAGGGTCCTCCAACTCTGCAGGAAGAGGAAGTGATCC
ACCTGTTTGGGGGCACCCAGCATACCCCCTGTACCAGGTGGACAGCGAAGTTCCCTCCATCATACATTTCATGGACATCT
TCTACTGCCAGAGAGGTCACTGTTCTGCATGGTAGACCACTTCCTGGCTCATGATCTGGAGTTTGACCAAGTGTACCAAT
ACAAGGATGCGATGGAGGTCATTCAAGATGCCACACAAGACATGACCTCATATACCAGCGGATTGAGTGGGGACCTAGAG
AAGTACATCCCCAAAATGAAGTAAATATTGCTATCCTGAGCCACCTGGTGGCCCATGGGAAACAGCTGTTCCTCATCACC
AACAGTCCCTTCAGCTTCGTAGACATGGAGATGTATCATATGGTGGGTCTTGATTGGTCAACCCTTCAATGAGGTTATCC
TCCAAGTGCACAAGTCCAGCTTTTTTCACCAACCAGCACAGTATTGCAGAAAACTCAATCAAAAGGGCTTAGTCCAGTGG
GAC

Alignment

ORF - retro_ttru_1120 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 56.03 %
• Parental protein coverage: 53.01 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 8

Retrocopy - Parental Gene Alignment:

Parental  LNPAAIYANNEISLRDVEVYGFDYDYTLAQYADTLHPEIFTAARDILIEHYKYPEGIRKYDYN-PSFAIR
          LN.AA.YA.NE....DV.VY...Y...LAQ....LH..I..AA.DILIE.YK..EGI.KYDYN.P.....
Retrocopy LNLAAVYASNEMNMSDVRVYSSHYEEMLAQNTAALHLAIYSAAHDILIEQYKCSEGIQKYDYN<PLVCLW

Parental  GLHYDIQKSLLMKIDAFHYVQLGTAYRGLQ-PVPDEEVIDLYGGTQH-IPLYQMSGFYGKGPSIKQFMDI
          GLHYDIQKS..MK.DAFHY.QLG.A.R.LQ.....EEVI.L.GGTQH..PLYQ........PSI..FMDI
Retrocopy GLHYDIQKSIQMKNDAFHYMQLGNASRVLQ<TLQEEEVIHLFGGTQH<YPLYQVD---SEVPSIIHFMDI

Parental  F-SLPEMALLSCVVDHFLGHGLEFDQAHLYKDVTDAIRDV-HVK-GLMYQWIE-RDMEKYILR-GDETFA
          F..LPE..L..C.VDHFL.H.LEFDQ...YKD....I.D..H....L.YQ.IE..D.EKYI........A
Retrocopy F<LLPERSLF-CMVDHFLAHDLEFDQVYQYKDAMEVIQDA<HTRHDLIYQRIE>GDLEKYIPK<NEVNIA

Parental  VLSRLVAHGKQLFLITNSPFSFVDKGMRHMVGADWRQL-FDVVIVQADKPSFFTDRRKPFRKLDEKGSLH
          .LS.LVAHGKQLFLITNSPFSFVD..M.HMVG.DW..L...V...Q..K.SFF.......RKL..KG...
Retrocopy ILSHLVAHGKQLFLITNSPFSFVDMEMYHMVGLDWSTL>NEVIL-QVHKSSFFHQPAQYCRKLNQKGLVQ

Parental  WD
          WD
Retrocopy WD

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_1120 retrocopy.

TSS

Tursiops truncatus was not studied using FANTOM5 data.

Lab

retro_ttru_1120 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 6 parental genes, and 6 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000008538	1 retrocopy	retro_amel_278,
Canis familiaris	ENSCAFG00000009184	1 retrocopy	retro_cfam_418,
Equus caballus	ENSECAG00000015835	1 retrocopy	retro_ecab_805,
Myotis lucifugus	ENSMLUG00000015418	1 retrocopy	retro_mluc_1559,
Tursiops truncatus	ENSTTRG00000008562	1 retrocopy	retro_ttru_1120 ,
Tursiops truncatus	ENSTTRG00000009239	1 retrocopy	retro_ttru_1040,