RetrogeneDB ID: retro_ttru_675

Retrocopy location

• Organism: Dolphin (Tursiops truncatus)
• Coordinates: GeneScaffold_3056:123645..124403(-)
• Located in intron of: ENSTTRG00000001491

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSTTRG00000014225
• Aliases: None
• Description: None

Sequence

>retro_ttru_675
AAGTCAGAGTCACCCAAAGAGCCCGAACAGCTGTGGAAGCTCTTCATCGGAGGTTTGAACTTTGAAACAACCGACGACAG
TCTGAGGAGCCATTGTGAGCAGTGGGGAGCGCTCACAGACTGTGTGGTGTTGAGGGATCCAAACACCAGGCACTCCAGGG
GCTTCGGGGTTGCCACATAAGCCACTGTGGAGGACGTGGACGCGGCCATGAATGCAAGGCCACACGAGGTGGATGGGAGA
GCTGTGGAACCAGAGGGCCGTCTCAAGGGAAGATTCTCAAAGACCTGGTGCCCGCTTAACTGTGAAAAAGATTTTTGTTG
GTGGCATTAAAGAAGACACTGACAAACATCACCTAAGAGATTATTTTGAACAGTATGGGAAAACTGAAGTGATTGAAATC
GTGACTGATCGAGGCAGTGGCAAAAAAGAGAGGCTTTGCTTTCGTAACCTTTGATGACCATGACTCCGTAGACAAGACTG
TCATTCAGAAATAGCACACTGTGAATGGCCACAACTGTGAAGTCAGGAAAGCCCTATCTAAGCGAGAGATGGCTAGTGCC
TCATCCAGCCAAAGGGGTCGAAGTGGGTCTGGAAGCTTTGGTGGTGGTCGTGGAGGGGGTTTTGGTGGGAGTGACAGCTT
TGGTCATGGAGGAGACTTCAGCGGCCGAGGTGGCTTTGGTGGCAGCCGCGGTGGCGGTGGCTATGGTGGCAGTGGAAATG
GCTATAATGGGTTTGGTAACGATGGAAGCCATTTTGGA

Alignment

ORF - retro_ttru_675 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 64.73 %
• Parental protein coverage: 67.28 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  EGHDPKEPEQLRKLFIGGLSFETTDDSLREHFEKWGTLTDCVVMRDPQTKRSRGFGFVTYSCVEEVDAAM
          ....PKEPEQL.KLFIGGL.FETTDDSLR.H.E.WG.LTDCVV.RDP.T..SRGFG..T...VE.VDAAM
Retrocopy KSESPKEPEQLWKLFIGGLNFETTDDSLRSHCEQWGALTDCVVLRDPNTRHSRGFGVAT*ATVEDVDAAM

Parental  CARPHKVDGRVVEPKRAVSREDSVKPGAHLTVKKIF-VGGIKEDTEEYNLRDYFEKYGKIETIEVMEDRQ
          .ARPH.VDGR.VEP........S.K....L...K.F.VGGIKEDT....LRDYFE.YGK.E.IE...DR.
Retrocopy NARPHEVDGRAVEPEGRLKGRFS-KTWCPLNCEKDF>VGGIKEDTDKHHLRDYFEQYGKTEVIEIVTDRG

Parental  SG-KKRGFAFVTFDDHDTVDKIVVQKYHTINGHNCEVKKALSKQEMQSA-GSQRGRGGGSGNFMGRGGNF
          SG.KKRGFAFVTFDDHD.VDK.V.QK.HT.NGHNCEV.KALSK.EM.SA..SQRGR.G......GRGG.F
Retrocopy SG>KKRGFAFVTFDDHDSVDKTVIQK*HTVNGHNCEVRKALSKREMASASSSQRGRSGSGSFGGGRGGGF

Parental  GGGGGNFGRGGNFGGRGGYGGGGGGSRGSYGGGDGGYNGFGGDGGNYG
          .GG...FG.GG.F.GRGG.GG..GG..G.YGG...GYNGFG.DG...G
Retrocopy -GGSDSFGHGGDFSGRGGFGGSRGG--GGYGGSGNGYNGFGNDGSHFG

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_675 retrocopy.

TSS

Tursiops truncatus was not studied using FANTOM5 data.

Lab

retro_ttru_675 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 19 parental genes, and 76 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000011920	4 retrocopies	retro_amel_1407, retro_amel_557, retro_amel_715, retro_amel_765,
Cavia porcellus	ENSCPOG00000004251	3 retrocopies	retro_cpor_1516, retro_cpor_1543, retro_cpor_65,
Ficedula albicollis	ENSFALG00000003215	1 retrocopy	retro_falb_15,
Gallus gallus	ENSGALG00000009250	1 retrocopy	retro_ggal_10,
Monodelphis domestica	ENSMODG00000019803	1 retrocopy	retro_mdom_1590,
Mustela putorius furo	ENSMPUG00000014103	6 retrocopies	retro_mputfur_1141, retro_mputfur_1336, retro_mputfur_1545, retro_mputfur_603, retro_mputfur_674, retro_mputfur_779,
Oryctolagus cuniculus	ENSOCUG00000002743	2 retrocopies	retro_ocun_994, retro_ocun_995,
Pelodiscus sinensis	ENSPSIG00000003011	1 retrocopy	retro_psin_16,
Pan troglodytes	ENSPTRG00000012676	5 retrocopies	retro_ptro_1059, retro_ptro_2430, retro_ptro_2966, retro_ptro_683, retro_ptro_872,
Rattus norvegicus	ENSRNOG00000001556	11 retrocopies	retro_rnor_1510, retro_rnor_1665, retro_rnor_1869, retro_rnor_2053, retro_rnor_2659, retro_rnor_2669, retro_rnor_2713, retro_rnor_2776, retro_rnor_2809, retro_rnor_348, retro_rnor_959,
Sarcophilus harrisii	ENSSHAG00000018255	1 retrocopy	retro_shar_518,
Tarsius syrichta	ENSTSYG00000012949	2 retrocopies	retro_tsyr_1480, retro_tsyr_2122,
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,
Xenopus tropicalis	ENSXETG00000001806	1 retrocopy	retro_xtro_11,
Xiphophorus maculatus	ENSXMAG00000000439	1 retrocopy	retro_xmac_2,