RetrogeneDB ID: retro_ttru_1591

Retrocopy location

• Organism: Dolphin (Tursiops truncatus)
• Coordinates: scaffold_401:5075..5705(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: EIF4E
• Ensembl ID: ENSTTRG00000004206
• Aliases: None
• Description: eukaryotic translation initiation factor 4E [Source:HGNC Symbol;Acc:3287]

Sequence

>retro_ttru_1591
GAAACCACCCCTACACCTAATCCCCCACCTACAGAAGAAGAGAAAACAGAATCTCATCAGGAGGTTGCTAACCCAGAACG
CTATATTAAACATCCTTTACAGAACAGATGGACACTCTGGAGTTTTTAAAATGATAAAAGCAAAACTTGGCAAGCAAACC
TTCGGCTGATCTCTAAGTCTGATACTGTTGACGACTTTTGGGCTCTGTACACCCATATCCAGTTGTCTAGCAGTTTAATG
CCTGGCTGTGACTACGCACTTTTTAAGGATGGTATTGAGCCTATGTGGGAAGATGAGAAAAACAAACGAGGAGGACGATG
GCTAATTACATTGAACAAACAGCAGAGACCAAGTGACCTCGATTGCTTTCGGCTAGAGACACTGCTGTGCCTTATTGGAG
AATCTTTTGATGACTACAGTGATGATGTATGTGGAGCTGTTAATGTTAGAGCTAAAGGTGAAAAAATAGCAATGTGGACT
ACTGAATGTGAAAACTGAGAAGCTGTTACACATATAGGGAGGGTAGACAAGGAAAGGTTAGGACTTCCTCCAAGGACAGT
GATTGGTTACCAGTCCCATGCAGACACAGCTACTCAGAGCGGCTCCAGCACTAAAAATAGGTTTGCTGTT

Alignment

ORF - retro_ttru_1591 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 89.1 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  ETTPTPNPPPTEEEKTESNQEVANPEHYIKHPLQNRWALWFFKNDKSKTWQANLRLISKFDTVEDFWALY
          ETTPTPNPPPTEEEKTES.QEVANPE.YIKHPLQNRW.LW.F.NDKSKTWQANLRLISK.DTV.DFWALY
Retrocopy ETTPTPNPPPTEEEKTESHQEVANPERYIKHPLQNRWTLWSF*NDKSKTWQANLRLISKSDTVDDFWALY

Parental  NHIQLSSNLMPGCDYSLFKDGIEPMWEDEKNKRGGRWLITLNKQQRRSDLDRFWLETLLCLIGESFDDYS
          .HIQLSS.LMPGCDY.LFKDGIEPMWEDEKNKRGGRWLITLNKQQR.SDLD.F.LETLLCLIGESFDDYS
Retrocopy THIQLSSSLMPGCDYALFKDGIEPMWEDEKNKRGGRWLITLNKQQRPSDLDCFRLETLLCLIGESFDDYS

Parental  DDVCGAVVNVRAKGDKIAIWTTECENKEAVTHIGRVYKERLGLPPKIVIGYQSHADTATKSGSTTKNRFV
          DDVCGA.VNVRAKG.KIA.WTTECEN.EAVTHIGRV.KERLGLPP..VIGYQSHADTAT.SGS.TKNRF.
Retrocopy DDVCGA-VNVRAKGEKIAMWTTECEN*EAVTHIGRVDKERLGLPPRTVIGYQSHADTATQSGSSTKNRFA

Parental  V
          V
Retrocopy V

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_1591 retrocopy.

TSS

Tursiops truncatus was not studied using FANTOM5 data.

Lab

retro_ttru_1591 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 38 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000009522	3 retrocopies	retro_btau_1094, retro_btau_1702, retro_btau_944,
Canis familiaris	ENSCAFG00000010307	1 retrocopy	retro_cfam_1276,
Choloepus hoffmanni	ENSCHOG00000009450	9 retrocopies	retro_chof_1177, retro_chof_1219, retro_chof_124, retro_chof_1319, retro_chof_1551, retro_chof_200, retro_chof_604, retro_chof_918, retro_chof_992,
Dasypus novemcinctus	ENSDNOG00000013712	5 retrocopies	retro_dnov_1722, retro_dnov_2378, retro_dnov_2570, retro_dnov_353, retro_dnov_638,
Echinops telfairi	ENSETEG00000007347	3 retrocopies	retro_etel_1285, retro_etel_1449, retro_etel_499,
Macropus eugenii	ENSMEUG00000011104	3 retrocopies	retro_meug_2087, retro_meug_2114, retro_meug_428,
Myotis lucifugus	ENSMLUG00000005035	3 retrocopies	retro_mluc_1519, retro_mluc_24, retro_mluc_474,
Monodelphis domestica	ENSMODG00000020716	1 retrocopy	retro_mdom_701,
Mustela putorius furo	ENSMPUG00000002041	1 retrocopy	retro_mputfur_37,
Otolemur garnettii	ENSOGAG00000001131	1 retrocopy	retro_ogar_259,
Tursiops truncatus	ENSTTRG00000004206	2 retrocopies	retro_ttru_1591 , retro_ttru_592,
Tursiops truncatus	ENSTTRG00000010927	2 retrocopies	retro_ttru_1799, retro_ttru_1920,
Vicugna pacos	ENSVPAG00000006072	3 retrocopies	retro_vpac_238, retro_vpac_444, retro_vpac_93,
Drosophila melanogaster	FBgn0035709	1 retrocopy	retro_dmel_68,