RetrogeneDB ID: retro_ttru_1440

Retrocopy location

• Organism: Dolphin (Tursiops truncatus)
• Coordinates: scaffold_113288:19592..20600(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: HIF1AN
• Ensembl ID: ENSTTRG00000004176
• Aliases: None
• Description: hypoxia inducible factor 1, alpha subunit inhibitor [Source:HGNC Symbol;Acc:17113]

Sequence

>retro_ttru_1440
GCGACTGCGGTGGAGGCTGCAGCCTCAGGCTCTGGAGAACCCCAGGAAGAGGCCAAAGCCCCTGGCCCCGCCTGGGATGA
ATCCCAACTACTCAGTTATACCTTCGCGACCTGGCCCATCCCGCATCTCAGTCAGAGCAACCCCGGGGACAGAGGAGCTT
ATTGAGAATGAGGAGCCTGTGGTGCTGGCAGACACAAATCTTGTGTATCCTGCCCTAAAATGGGGCCTTTGAATAACTGC
GAGAAAATATTGACACAGAGACTTCTCTGTGTACAGTGCCAGCACCCACAAGTTCTTGCACTATGATGAAAAAGAAGATG
GCTAATTTCCAGAACTTTAAGCTGAGGTCCAATAGGTGAAGAAATGAAATTTCATGAGTTTGTTGAGCAACGGCAGAATA
TACAGCAGTGAGGAGGTGAAGAGAGCTCGTATCTGCAGCAAACACTCAATGACACTGTGAGCAGGAAGATTGTCATGGAC
TTCTTGGGTTTTGACTGGAACTGGATTAATAAGCAACAGGGAAAGCGTGGCTGGGGGCAGCTGACCTGTAACCTGCTGCT
TATTGGCATGGAAGGAAATGTGACACCTGCTCACTATGATGAGCAACAGAACTTCTTTGCTCAGATAAAAGGTACAAGCG
ATGCATTTTGTTCCCTCCGGGTCAGTTTGAGTGCCTCTACGCATATCCTGTTCATCATCCATGTGACAGACAGAGCCAGG
TGGACTTTGACAATCCTGACTACAAGAGGTTCCCCAATTTCCAGAATGTGGTTGGTTACGAAAGAGTGGTTGGCCCTGGT
GATGTTCTTTACATCTGAATGTACTGGTGGCATCACAGAGTCATTACTAAATGGGGGCACTACCATCACTGTGTACTTCT
GGTATTAGGGGGCCCCCATCCCTAAGAGAACTGAATATCCTCTCAAAGCCCATCAGAAAGTGGCCATAATGAGAAACATT
GAGAAGATGCTTGGAGAGGCCTTGGGGAACCCACAAGAGACTGTTCCC

Alignment

ORF - retro_ttru_1440 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 85.13 %
• Parental protein coverage: 96.28 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 7

Retrocopy - Parental Gene Alignment:

Parental  ATAAEAAASGSGEPREEAEAPGPAWDESQLRSYTFPTRPIPRLSQSDPR-AEELIENEEPVVLTDTNLVY
          ATA.EAAASGSGEP.EEA.APGPAWDESQL.SYTF.T.PIP.LSQS.P...EELIENEEPVVL.DTNLVY
Retrocopy ATAVEAAASGSGEPQEEAKAPGPAWDESQLLSYTFATWPIPHLSQSNPG>TEELIENEEPVVLADTNLVY

Parental  PALKWDL-EYLQENIG-NGDFSVYSASTHKFLYYDEK-KMANFQNFKPRSNR-EEMKFHEFVEKLQDIQE
          PALKW.L.E.L.ENI....DFSVYSASTHKFL.YDEK.KMANFQNFK.RSNR.EEMKFHEFVE..Q.IQ.
Retrocopy PALKWGL>E*LRENID<HRDFSVYSASTHKFLHYDEK>KMANFQNFKLRSNR>EEMKFHEFVEQRQNIQQ

Parental  RGGEERLYLQQTLNDTVGRKIVMDFLGFNWNWINKQQGKRGWGQLTSNLLLIGMEGNVTPAHYDEQQNFF
          .GGEE..YLQQTLNDTV.RKIVMDFLGF.WNWINKQQGKRGWGQLT.NLLLIGMEGNVTPAHYDEQQNFF
Retrocopy *GGEESSYLQQTLNDTVSRKIVMDFLGFDWNWINKQQGKRGWGQLTCNLLLIGMEGNVTPAHYDEQQNFF

Parental  AQIKG-YKRCILFPPDQFECLYPYPVHHPCDRQSQVDFDNPDYERFPNFQNVVGYETVVGPGDVLYIPMY
          AQIKG.YKRCILFPP.QFECLY.YPVHHPCDRQSQVDFDNPDY.RFPNFQNVVGYE.VVGPGDVLYI.MY
Retrocopy AQIKG<YKRCILFPPGQFECLYAYPVHHPCDRQSQVDFDNPDYKRFPNFQNVVGYERVVGPGDVLYI*MY

Parental  WWHH-IESLLNGGITITVNFWYKGAPTPKRIEYPLKAHQKVAIMRNIEKMLGEALGNPQEVGP
          .W.H..ESLLNGG.TITV.FWY.GAP.PKR.EYPLKAHQKVAIMRNIEKMLGEALGNPQE..P
Retrocopy -WWH>TESLLNGGTTITVYFWY*GAPIPKRTEYPLKAHQKVAIMRNIEKMLGEALGNPQETVP

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_1440 retrocopy.

TSS

Tursiops truncatus was not studied using FANTOM5 data.

Lab

retro_ttru_1440 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
Mustela putorius furo	ENSMPUG00000016956	1 retrocopy	retro_mputfur_120,
Tursiops truncatus	ENSTTRG00000004176	1 retrocopy	retro_ttru_1440 ,