RetrogeneDB ID: retro_ttru_1366

Retrocopy location

• Organism: Dolphin (Tursiops truncatus)
• Coordinates: scaffold_111431:64487..65591(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: EWSR1
• Ensembl ID: ENSTTRG00000011881
• Aliases: None
• Description: EWS RNA-binding protein 1 [Source:HGNC Symbol;Acc:3508]

Sequence

>retro_ttru_1366
CCAGGAGAGAACCAGAGCATGAGTGGCCCTGATAACCAAGGCAGTGGAAGAGGAGGATTTGATCCTGGAAGCATGAACAC
AGGTGGATGGGGAAGAGGACATGGTGGAATGGGCACTGAAGAGCCAGGTGGCTTCAATAAGCCTGATGGACCCATAGATG
AAGGACTAGATCTTGATTTAGGCCCACCTGCAGATCCAGATGAAGACTCTGACAACAGTGCAATTTATGTGCAGGAATTA
AATGACAGTGTGACTCTAGATGATCTGGCAGACTTCTTTAAGGAGTGTGGAGTTGTTAAGGTGAACAAGAGGACTGGACA
ACCCATGATTCATATATACTTGGACAAGGAAACAGGAAAGGCCAAAGGTGATGCTACAGTGTCCTATGAAGACCCATCAA
CTGCCAATACTGCTGTCGAGTGGTTTGATGGGAAGGATTTTTCAAGGGAGCAAACTTAAAATTTCTCTGGCTTGGAAGAA
GCCTCCAATGAACAGCATGCAGGGAGGAATGCAGCCACCCCGTGAGGGCAGAGGGATGGCACCACATCTCCGAGGAGGTC
CAAGGGACCCGGGAGGTCCTAGAGGACCCATGGGTTACATGGGAGGCTGAGGAGGAGACAGAGGAGGCTTCCCACAAAGA
GGGCCCTGCAGTTCTCAAGGGAACCTGTCTGGAGGAAGAAAGGTCCAGCACCAAGCTGGAGACTGGCAGTGCCCCAATCA
GGGGTGTGTAAAGCAGAACTTCACCTGTAGAACAGAGTGCAACCAGTGTAAGGCCCCAAAGCCTGAAGGTTTTCTCCCAC
CACCTTTCCCACCCCCGGGCAGTGACCATGGCAGAGGTGGCCCTGGTAGCATGCTGAGAGCACGAGGTGGCCTCATGTAC
CATAGTGGTTCTAGTGGAATGTTCAGAGGTGGCTGTGGTGGAGACAGAGGTGGCTTCTGTGATGGTCAGGGCATGGACAA
AGGGTGGCTTTTGTGGAGGAAGACAAGGTGGCCTAGGGGACACCCTGGACCTTTGATGGAACAGATGGGAGGAATAAGAG
GCAGGAGTGAAGACATGGGAAAATGGATAAAAGTGAGCATCATCAGGAATGCAGAGACTGACCT

Alignment

ORF - retro_ttru_1366 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 77.21 %
• Parental protein coverage: 55.59 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  PGENRSMSGPDNRGRGRGGFDRGGMSRGGRGGGRGGMGSAGERGGFNKPGGPMDEGPDLDLGPPVDPDED
          PGEN.SMSGPDN.G.GRGGFD.G.M..GG.G.G.GGMG...E.GGFNKP.GP.DEG.DLDLGPP.DPDED
Retrocopy PGENQSMSGPDNQGSGRGGFDPGSMNTGGWGRGHGGMGTE-EPGGFNKPDGPIDEGLDLDLGPPADPDED

Parental  CDNSAIYVQGLSDSVTLDDLADFFKQCGVVKINKRTGQPMIHIYLDKETGKPKGDATVSYEDPPTAKTAV
          .DNSAIYVQ.L.DSVTLDDLADFFK.CGVVK.NKRTGQPMIHIYLDKETGK.KGDATVSYEDP.TA.TAV
Retrocopy SDNSAIYVQELNDSVTLDDLADFFKECGVVKVNKRTGQPMIHIYLDKETGKAKGDATVSYEDPSTANTAV

Parental  EWFDGKDF-QGSKLKVSLARKKPPMNSMRGGM-PPREGRGMPPPLRGGPGGPGGPGGPMGRMGGRGGDRG
          EWFDGKDF.QGSKLK.SLA.KKPPMNSM.GGM.PPREGRGM.P.LRGGP..PGGP.GPMG.MGG.GGDRG
Retrocopy EWFDGKDF>QGSKLKISLAWKKPPMNSMQGGMQPPREGRGMAPHLRGGPRDPGGPRGPMGYMGG*GGDRG

Parental  GFPPRGPRGSRGNPSGGGNVQHRAGDWQCPNPGCGNQNFAWRTECNQCKAPKPEGFLPPPFPPPGGDRGR
          GFP.RGP..S.GN.SGG..VQH.AGDWQCPN.GC..QNF..RTECNQCKAPKPEGFLPPPFPPPG.D.GR
Retrocopy GFPQRGPCSSQGNLSGGRKVQHQAGDWQCPNQGCVKQNFTCRTECNQCKAPKPEGFLPPPFPPPGSDHGR

Parental  GGPGGMRGGRGGLMDRGGPGGMFRGGRGGDRGGFRGTRGMD-RGGFGGGRRGG-PGGPPGPLMEQMGGRR
          GGPG.M...RGGLM...G..GMFRGG.GGDRGGF....GMD..GGF.GGR.GG.P.G.PGPLMEQMGG.R
Retrocopy GGPGSMLRARGGLMYHSGSSGMFRGGCGGDRGGFCDGQGMD>KGGFCGGRQGG<PRGHPGPLMEQMGGIR

Parental  GGRGGPG-KMDKGEHRQERRDRP
          G.....G.KMDK.EH.QE.RD.P
Retrocopy GRSEDMG<KMDKSEHHQECRD*P

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_1366 retrocopy.

TSS

Tursiops truncatus was not studied using FANTOM5 data.

Lab

retro_ttru_1366 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.

---

Parental genes homology:

Parental genes homology involve 13 parental genes, and 25 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000008298	2 retrocopies	retro_amel_191, retro_amel_959,
Canis familiaris	ENSCAFG00000012160	8 retrocopies	retro_cfam_1142, retro_cfam_1183, retro_cfam_1225, retro_cfam_133, retro_cfam_1397, retro_cfam_1736, retro_cfam_1889, retro_cfam_560,
Callithrix jacchus	ENSCJAG00000019987	4 retrocopies	retro_cjac_1716, retro_cjac_2022, retro_cjac_2813, retro_cjac_2911,
Homo sapiens	ENSG00000182944	1 retrocopy	retro_hsap_463,
Gorilla gorilla	ENSGGOG00000012212	1 retrocopy	retro_ggor_444,
Macropus eugenii	ENSMEUG00000008703	1 retrocopy	retro_meug_1424,
Myotis lucifugus	ENSMLUG00000012058	1 retrocopy	retro_mluc_328,
Monodelphis domestica	ENSMODG00000008679	1 retrocopy	retro_mdom_279,
Oryctolagus cuniculus	ENSOCUG00000004432	2 retrocopies	retro_ocun_1346, retro_ocun_242,
Pongo abelii	ENSPPYG00000011684	1 retrocopy	retro_pabe_1769,
Pan troglodytes	ENSPTRG00000014218	1 retrocopy	retro_ptro_350,
Ictidomys tridecemlineatus	ENSSTOG00000023177	1 retrocopy	retro_itri_1892,
Tursiops truncatus	ENSTTRG00000011881	1 retrocopy	retro_ttru_1366 ,