RetrogeneDB ID: retro_ttru_9

Retrocopy location

• Organism: Dolphin (Tursiops truncatus)
• Coordinates: GeneScaffold_1989:768042..768954(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSTTRG00000000499
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

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

Sequence

>retro_ttru_9
ATGGAGAATTCCCAGCTGTGTAAGCTGTTCATCGGCGGCCTCAACGTGCAGACGAGTGAGTCGGGCCTGCGCGGCCACTT
TGAGGCCTTTGGGACCCTGACGGACTGCGTGGTGGTGGTGAACCCCCAGACCAAGCGCTCCCGTTGCTTCGGCTTCGTGA
CCTACTCCAATGTGGAGGAGGCCGATGCCGCCATGGCCGCCTCGCCCCATGCCGTGGACGGCAACACGGTGGAGCTGAAG
CGGGCGGTGTCCCGGGAGGATTCGGCGCGGCCCGGTGCCCACGCCAAGGTGAAGAAGCTCTTTGTCGGGGGCCTTAAGGG
AGACGTGGCCGAGGGCGACCTGATAGAGCACTTCTCGCAGTTTGGCACCGTGGAAAAGGCCGAGATTATTGCCGACAAGC
AGTCTGGCAAGAAGCGTGGTTTCGGCTTCGTGTATTTTCAGAATCACGACGCGGCAGACAAGGCCGCGGTGGTCAAGTTC
CATCCGATCCAGGGCCATCGCGTGGAGGTGAAGAAGGCTGTCCCCAAGGAGGATATCCACTCCGGTGGGGGCGGAGGCGG
CTCCCGCTCCTCCCGGGGCGGCCGGGGCGGTCGGGGTCGGGGCGGTGGTCGTGACCAGAACGGCCTGTCTAAGGGCGGCG
GCGGCTACAACAGCTACGGTGGTTACGGCGGCGGCGGTGGCTACAACGCCTATGGAGGCGGCGGAGGCGGTTCGTCCTAC
GGTGGAAGCGACTACGGTAACGGCTTCGGCGGCTTCGGTAGCTACAGCCAGCACCAGTCGTCCTATGGGCCCATGAAGAG
CGGTGGCGGCGGCGGCGGTGGAGGAGGCAGCAGCTGGGGAGGTCGCAGTAACAGTGGACCTTACAGAGGTGGCTATGGCG
GTGGGGGTGGGTATGGAGGCAGCTCCTTCTAA

Alignment

ORF - retro_ttru_9 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 54.28 %
• Parental protein coverage: 79.42 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  EPEQLRKLFIGGLSFETTDDSLREHFEKWGTLTDCVVMRDPQTKRSRGFGFVTYSCVEEVDAAMCARPHK
          E..QL.KLFIGGL...T....LR.HFE..GTLTDCVV...PQTKRSR.FGFVTYS.VEE.DAAM.A.PH.
Retrocopy ENSQLCKLFIGGLNVQTSESGLRGHFEAFGTLTDCVVVVNPQTKRSRCFGFVTYSNVEEADAAMAASPHA

Parental  VDGRVVEPKRAVSREDSVKPGAHLTVKKIFVGGIKEDTEEYNLRDYFEKYGKIETIEVMEDRQSGKKRGF
          VDG..VE.KRAVSREDS..PGAH..VKK.FVGG.K.D..E..L...F...G..E..E...D.QSGKKRGF
Retrocopy VDGNTVELKRAVSREDSARPGAHAKVKKLFVGGLKGDVAEGDLIEHFSQFGTVEKAEIIADKQSGKKRGF

Parental  AFVTFDDHDTVDKIVVQKYHTINGHNCEVKKALSKQEMQSAGSQRGRGGGSGNFMGRGGNFGGGGGNFGR
          .FV.F..HD..DK..V.K.H.I.GH..EVKKA..K....S.G.....GGGS....G..G..G.GGG....
Retrocopy GFVYFQNHDAADKAAVVKFHPIQGHRVEVKKAVPKEDIHSGGG----GGGSRSSRGGRGGRGRGGGRDQN

Parental  GGNFGGRG--GYGG-GGGGSRGSYGGGDGGYNGFGGDGGNYGGGPGYSSRGGYGGGGPGYGNQGGGYGGG
          G...GG.G...YGG.GGGG....YGGG.GG....G.D.GN..GG.G..S......G....G..GGG.GGG
Retrocopy GLSKGGGGYNSYGGYGGGGGYNAYGGGGGGSSYGGSDYGNGFGGFGSYSQHQSSYGPMKSG--GGGGGGG

Parental  GGGYDGYNEGGNFGGGNYGGGGSY
          G....G....G...GG.YGGGG.Y
Retrocopy GSSWGGRSNSGPYRGG-YGGGGGY

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_9 retrocopy.

TSS

Tursiops truncatus was not studied using FANTOM5 data.

Lab

retro_ttru_9 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,