RetrogeneDB ID: retro_ttru_1913

Retrocopy location

• Organism: Dolphin (Tursiops truncatus)
• Coordinates: scaffold_98524:1549..2151(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: HNRNPD
• Ensembl ID: ENSTTRG00000007592
• Aliases: None
• Description: heterogeneous nuclear ribonucleoprotein D (AU-rich element RNA binding protein 1, 37kDa) [Source:HGNC Symbol;Acc:5036]

Sequence

>retro_ttru_1913
GCACGGCAAGAAGAATGGAAAATGTTTATAGGAGGCCTTAGCTGGGATACTACAAAGAAAGATCTGAAGGACTACTACTC
CAAATTTGGTGAAGTTGTAGACTGCACTCTGAAGTTAGATCTTATCACAGAGCGATCAAGGGGTTTTGGCTTTGTGCTAT
TTAAAGAGTCGGAGAGTGTAGATAAGGTCATGGATCAGAAAGAACATAAATTGAATGGGAAGGTGATTGATCCTAAGAGG
GCCAAAGTCATGAAAACAAAAGAGCCTGTTAAAAAATTTTTGTTGGTGGCCTTTCTCCAGATACACCTGAAGAGAAAATA
AGGGAGTATTTTGGTGGTTTTGGTGAGGTTGAATCCATAGAGCTCCCCATGGACAACAAGACCAATAAGAGGTGTGGATT
CTGTTTTATTACCTTTAAGGAAGAAGAACCAGTGAAGAAGATAATGGAAAAGAAATACTACAATGTTGGTCTTAGTAAAT
GTGGAATAAAAGTAGCTATGTCGAAGGAACAGTGTCAGCAACAGCAACAGTGGGGATCTAGAGGAGGATTTCCGGGAAGA
GCTCATGGAAGAGATGGTGACCAGCAGAGTGGTTATGGGAAA

Alignment

ORF - retro_ttru_1913 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 89.11 %
• Parental protein coverage: 56.62 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  AQREEWKMFIGGLSWDTTKKDLKDYFSKFGEVVDCTLKLDPITGRSRGFGFVLFKESESVDKVMDQKEHK
          A..EEWKMFIGGLSWDTTKKDLKDY.SKFGEVVDCTLKLD.IT.RSRGFGFVLFKESESVDKVMDQKEHK
Retrocopy ARQEEWKMFIGGLSWDTTKKDLKDYYSKFGEVVDCTLKLDLITERSRGFGFVLFKESESVDKVMDQKEHK

Parental  LNGKVIDPKRAKAMKTKEPVK-KIFVGGLSPDTPEEKIREYFGGFGEVESIELPMDNKTNKRRGFCFITF
          LNGKVIDPKRAK.MKTKEPVK.KIFVGGLSPDTPEEKIREYFGGFGEVESIELPMDNKTNKR.GFCFITF
Retrocopy LNGKVIDPKRAKVMKTKEPVK<KIFVGGLSPDTPEEKIREYFGGFGEVESIELPMDNKTNKRCGFCFITF

Parental  KEEEPVKKIMEKKYHNVGLSKCEIKVAMSKEQYQQQQQWGSRGGFAGRARGRGGGPSQNWNQ
          KEEEPVKKIMEKKY.NVGLSKC.IKVAMSKEQ.QQQQQWGSRGGF.GRA.GR.G........
Retrocopy KEEEPVKKIMEKKYYNVGLSKCGIKVAMSKEQCQQQQQWGSRGGFPGRAHGRDGDQQSGYGK

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_1913 retrocopy.

TSS

Tursiops truncatus was not studied using FANTOM5 data.

Lab

retro_ttru_1913 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 14 parental genes, and 48 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000015165	1 retrocopy	retro_cjac_2796,
Dipodomys ordii	ENSDORG00000012507	1 retrocopy	retro_dord_649,
Homo sapiens	ENSG00000138668	1 retrocopy	retro_hsap_4689,
Gorilla gorilla	ENSGGOG00000026760	1 retrocopy	retro_ggor_2916,
Loxodonta africana	ENSLAFG00000016483	1 retrocopy	retro_lafr_686,
Pan troglodytes	ENSPTRG00000016215	1 retrocopy	retro_ptro_3116,
Sarcophilus harrisii	ENSSHAG00000013312	1 retrocopy	retro_shar_752,
Tarsius syrichta	ENSTSYG00000010395	3 retrocopies	retro_tsyr_1092, retro_tsyr_2070, retro_tsyr_269,
Tursiops truncatus	ENSTTRG00000000709	3 retrocopies	retro_ttru_1066, retro_ttru_1204, retro_ttru_1788,
Tursiops truncatus	ENSTTRG00000001793	2 retrocopies	retro_ttru_1486, retro_ttru_744,
Tursiops truncatus	ENSTTRG00000004505	27 retrocopies	retro_ttru_1202, retro_ttru_1223, retro_ttru_1251, retro_ttru_1331, retro_ttru_1362, retro_ttru_156, retro_ttru_157, retro_ttru_1678, retro_ttru_1732, retro_ttru_1806, retro_ttru_1813, retro_ttru_1874, retro_ttru_221, retro_ttru_311, retro_ttru_479, retro_ttru_599, retro_ttru_605, retro_ttru_607, retro_ttru_620, retro_ttru_63, retro_ttru_678, retro_ttru_708, retro_ttru_812, retro_ttru_882, retro_ttru_902, retro_ttru_926, retro_ttru_981,
Tursiops truncatus	ENSTTRG00000007592	1 retrocopy	retro_ttru_1913 ,
Tursiops truncatus	ENSTTRG00000014225	3 retrocopies	retro_ttru_1459, retro_ttru_675, retro_ttru_9,
Vicugna pacos	ENSVPAG00000004374	2 retrocopies	retro_vpac_484, retro_vpac_97,