RetrogeneDB ID: retro_ttru_1766

Retrocopy location

• Organism: Dolphin (Tursiops truncatus)
• Coordinates: scaffold_90887:86392..86983(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: HNRNPH3
• Ensembl ID: ENSTTRG00000013322
• Aliases: None
• Description: heterogeneous nuclear ribonucleoprotein H3 (2H9) [Source:HGNC Symbol;Acc:5043]

Sequence

>retro_ttru_1766
GGTTATGGAGGTTGTGATGACTATGGTGGCTATAATAATTCTGGTTATGGGCATGATGGCTTTGATGATAGAATGAGAGA
TGGAAGAGGTATGGGAGTTCCAGGCTATGGTGGAGCTGCTAATGTAAGTTCAGATTTTCATGGTGGTCATATTGTATATA
TGAGAAGATTACATTTTCATTCAATTGAAGATGACATTGCTAATTTCTTCCCAGCACTAAATCCAATACTAGTTTATACT
GATATTGGAGCTGATGGCAGAGCAACCAGAGAAGCAGATGTACAGTTTATGACACATGAAGTTGCAGTCGCTCGCCATGT
CTAAAGATATGAGTAACATACAACATCAATACATTGAATTCTTCTTGAATTCTAGTCCTGAGGTGGCTTTGGAATGGGAG
ATTCTGGAATGGGATGCTATGGCAGAGATGGAATGTATAAAAAGGGAGATTATGTATCTATTGGGAGAATGGGAATGATG
AACAACTTACAATGGAAGATACAGTATTCCTGTTGGCTTAGGTGGTGGTGGATGCAGTGGAGGTTACCATGGGCAAGATG
GCAAGAATGAGGTGAATGGTGTGTGATGTAC

Alignment

ORF - retro_ttru_1766 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 68.29 %
• Parental protein coverage: 58.09 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  GYGGFDDYGGYNNYGYGNDGFDDRMRDGRGMGGHGYGGAGDASSGFHGGHFVHMRGLPFRATENDIANFF
          GYGG.DDYGGYNN.GYG.DGFDDRMRDGRGMG..GYGGA...SS.FHGGH.V.MR.L.F...E.DIANFF
Retrocopy GYGGCDDYGGYNNSGYGHDGFDDRMRDGRGMGVPGYGGAANVSSDFHGGHIVYMRRLHFHSIEDDIANFF

Parental  SPLNPIRVHIDIGADGRATGEADVEFVTHEDAVA-AMSKDKNNMQHRYIELFLNSTPG-GGSGMGGSGMG
          ..LNPI.V..DIGADGRAT.EADV.F.THE.AVA.AMSKD..N.QH.YIE.FLNS.P..GG.GMG.SGMG
Retrocopy PALNPILVYTDIGADGRATREADVQFMTHEVAVA>AMSKDMSNIQHQYIEFFLNSSPE<GGFGMGDSGMG

Parental  AYGRDGMDNQGGYGSVGRMGMGNN-YSGGYGTPDGLGGYGRGGGGSGGYYGQGGMSG-GGWRGMY
          .YGRDGM...G.Y.S.GRMGM.NN.Y.G.Y..P.GLGG....GG.SGGY.GQ.G....G.W..MY
Retrocopy CYGRDGMYKKGDYVSIGRMGMMNN>YNGRYSIPVGLGG----GGCSGGYHGQDGKNE<GEWCVMY

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_1766 retrocopy.

TSS

Tursiops truncatus was not studied using FANTOM5 data.

Lab

retro_ttru_1766 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 11 parental genes, and 16 retrocopies.

Species	Parental gene accession	Retrocopies number
Anolis carolinensis	ENSACAG00000010365	1 retrocopy	retro_acar_184,
Ailuropoda melanoleuca	ENSAMEG00000018064	1 retrocopy	retro_amel_1375,
Bos taurus	ENSBTAG00000014316	2 retrocopies	retro_btau_1504, retro_btau_470,
Callithrix jacchus	ENSCJAG00000019154	2 retrocopies	retro_cjac_292, retro_cjac_578,
Equus caballus	ENSECAG00000007190	1 retrocopy	retro_ecab_912,
Gallus gallus	ENSGALG00000003947	1 retrocopy	retro_ggal_16,
Macropus eugenii	ENSMEUG00000013139	1 retrocopy	retro_meug_1627,
Mustela putorius furo	ENSMPUG00000011997	1 retrocopy	retro_mputfur_1469,
Oryctolagus cuniculus	ENSOCUG00000004443	3 retrocopies	retro_ocun_1136, retro_ocun_1379, retro_ocun_1615,
Tursiops truncatus	ENSTTRG00000013322	2 retrocopies	retro_ttru_1744, retro_ttru_1766 ,
Vicugna pacos	ENSVPAG00000011814	1 retrocopy	retro_vpac_403,