RetrogeneDB ID: retro_ttru_1662

Retrocopy location

• Organism: Dolphin (Tursiops truncatus)
• Coordinates: scaffold_84095:6098..7685(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: DDX5
• Ensembl ID: ENSTTRG00000008793
• Aliases: None
• Description: DEAD (Asp-Glu-Ala-Asp) box helicase 5 [Source:HGNC Symbol;Acc:2746]

Sequence

>retro_ttru_1662
GGTTATTCGAGTGACCGAGACTGCACCTGGGATCGAGGGTTTCGTGTCCCTCGATTTGGAGGAAGTAGGGCAGGGCCGTT
ATCTGGAAAGAAGTTTGGAAACCCTGGGGAGAAACTGGTTAAAAAGAAGTGGAATCTTGATGAGCTGTCCAAATTTGAGA
AGAATTTTTATCAAGAACACCCTGATTTGGCTAGGTGTACAGCACAAGAGGGAGAGACATACAGAAGAAGCAAGGAAATT
ACAGTTAGAGGTCACAACTGCCCAAAGCCAGTACTGAACTTTTATGAAGCGAACTTCCCACCAAATGTCATGGACGTGAT
TGCAAGGCAGAACTTTACTGAACCCACAGCTATTCAAGCTCAGGGATGGCCAGTTGCTCTAAATAGATTGGATATGGTTG
GGGTAGCAGAAACTGGACCTGGGAAGGCGTTGTCTTATTTGATGCCTGCCATTGTCCACATCAATCATCAGCCACTCCTA
GAGAGAGGTGACGGACCTATTTGCTTGGTGCTGGCACCAACTCGGGAACTGGCCCAACAGGTACAGCAAGTAGCTGCTGA
ATACTGTAGAGCATGTTGCTTGAAGTCCACTTGCATTTATCGTGGTGCTCCCAAGGGACCACAAATATGTTATTTGGAGA
GAGATGTAGAAATCTGTATTGCAACACCTGGAAGACTTACTGACTTTTTAGAATGTGGGAAAACCAATCTAAGAAGAACC
ACCTATCTTGTCCTTGATGAAGCAGACAGAATGCTTGATATGGGATTCGAACCTCAAATAAGGAAGATTGTGGATTAGAT
AAGACCTGATAGGCAAACCCTAATGTGGAGTGCTACTTGGCCAAAAGAAGTAAGACAGCTTGCTGAAGATTTCCTGAAAG
ACTATATTCATATAAACATTGGTGCACTAGAACTGAGTGCAAATCACAACATTCTTCAGATTGTGGATGTGTGTCATGAT
GTAGAAAAGGAAGAAAAGCTTATTCATTTAATGGAAGAGGTCATGAGTGAGAAGATGATTAAAACCATTGTTTTTGTTGA
AACCAAAAGTAGATGTGATGAACTCACTAGAAAAATGAGGATAGATGGGTGGCCTGTCATGGGTATCCATGGTGACAAGA
GTCAACAGGAACGTGACTGGGTTCTAAATGAATTCAAACATGGAAAGGCTCCTATTCTGATTGCTACAGATGTGGCCTCC
AGAGGGCTAGATGTGGAAGATGTGAAATTTGTCATCAATTATGACTACCCTAACTCCTCAGAGGATTACATTCATCGAAT
TGGAAGAACTGCTTGCAGTACCAAAACAGGCACAGCATACACTTTCTTTACACCTGATAACATAAAGCAAGTGAGTGACC
TTATCTCTGTGCTTCGTGAAGCTAATCAAGCAATTAATCCCAAATTGCTTCAGTTGGTCGAAGACAGAGGTTCAGGTCGT
TCCAGGGGTAGAGGAGGCATGAAGGATGACCATCGGGACAGATACTCTGTTGGCAAAAGGGGTGGATTTAATACATTTAG
AGACAGGGAAAATTATGACAGGTTACTCTAGTCTGCTTAAGAGAGATTTTGGGGCAAAAACTCAAAA

Alignment

ORF - retro_ttru_1662 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 91.12 %
• Parental protein coverage: 86.16 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  GYSSDRDRGRDRGFGAPRFGGSRAGPLSGKKFGNPGEKLVKKKWNLDELPKFEKNFYQEHPDLARRTAQE
          GYSSDRD...DRGF..PRFGGSRAGPLSGKKFGNPGEKLVKKKWNLDEL.KFEKNFYQEHPDLAR.TAQE
Retrocopy GYSSDRDCTWDRGFRVPRFGGSRAGPLSGKKFGNPGEKLVKKKWNLDELSKFEKNFYQEHPDLARCTAQE

Parental  VETYRRSKEITVRGHNCPKPVLNFYEANFPANVMDVIARQNFTEPTAIQAQGWPVALSGLDMVGVAQTGS
          .ETYRRSKEITVRGHNCPKPVLNFYEANFP.NVMDVIARQNFTEPTAIQAQGWPVAL..LDMVGVA.TG.
Retrocopy GETYRRSKEITVRGHNCPKPVLNFYEANFPPNVMDVIARQNFTEPTAIQAQGWPVALNRLDMVGVAETGP

Parental  GKTLSYLLPAIVHINHQPFLERGDGPICLVLAPTRELAQQVQQVAAEYCRACRLKSTCIYGGAPKGPQIR
          GK.LSYL.PAIVHINHQP.LERGDGPICLVLAPTRELAQQVQQVAAEYCRAC.LKSTCIY.GAPKGPQI.
Retrocopy GKALSYLMPAIVHINHQPLLERGDGPICLVLAPTRELAQQVQQVAAEYCRACCLKSTCIYRGAPKGPQIC

Parental  DLERGVEICIATPGRLIDFLECGKTNLRRTTYLVLDEADRMLDMGFEPQIRKIVDQIRPDRQTLMWSATW
          .LER.VEICIATPGRL.DFLECGKTNLRRTTYLVLDEADRMLDMGFEPQIRKIVD.IRPDRQTLMWSATW
Retrocopy YLERDVEICIATPGRLTDFLECGKTNLRRTTYLVLDEADRMLDMGFEPQIRKIVD*IRPDRQTLMWSATW

Parental  PKEVRQLAEDFLKDYIHINIGALELSANHNILQIVDVCHDVEKDEKLIRLMEEIMSEKENKTIVFVETKR
          PKEVRQLAEDFLKDYIHINIGALELSANHNILQIVDVCHDVEK.EKLI.LMEE.MSEK..KTIVFVETK.
Retrocopy PKEVRQLAEDFLKDYIHINIGALELSANHNILQIVDVCHDVEKEEKLIHLMEEVMSEKMIKTIVFVETKS

Parental  RCDELTRKMRRDGWPAMGIHGDKSQQERDWVLNEFKHGKAPILIATDVASRGLDVEDVKFVINYDYPNSS
          RCDELTRKMR.DGWP.MGIHGDKSQQERDWVLNEFKHGKAPILIATDVASRGLDVEDVKFVINYDYPNSS
Retrocopy RCDELTRKMRIDGWPVMGIHGDKSQQERDWVLNEFKHGKAPILIATDVASRGLDVEDVKFVINYDYPNSS

Parental  EDYIHRIGRTARSTKTGTAYTFFTPNNIKQVSDLISVLREANQAINPKLLQLVEDRGSGRSRGRGGMKDD
          EDYIHRIGRTA.STKTGTAYTFFTP.NIKQVSDLISVLREANQAINPKLLQLVEDRGSGRSRGRGGMKDD
Retrocopy EDYIHRIGRTACSTKTGTAYTFFTPDNIKQVSDLISVLREANQAINPKLLQLVEDRGSGRSRGRGGMKDD

Parental  RRDRYSAGKRGGFNTFRDRENYDRGYSSLLKRDFGAKTQ
          .RDRYS.GKRGGFNTFRDRENYDR...S...R..G....
Retrocopy HRDRYSVGKRGGFNTFRDRENYDRLL*SA*ERFWGKNSK

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_1662 retrocopy.

TSS

Tursiops truncatus was not studied using FANTOM5 data.

Lab

retro_ttru_1662 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 10 parental genes, and 16 retrocopies.

Species	Parental gene accession	Retrocopies number
Echinops telfairi	ENSETEG00000019950	1 retrocopy	retro_etel_1009,
Felis catus	ENSFCAG00000003512	1 retrocopy	retro_fcat_172,
Myotis lucifugus	ENSMLUG00000009496	4 retrocopies	retro_mluc_1136, retro_mluc_1499, retro_mluc_1845, retro_mluc_2208,
Monodelphis domestica	ENSMODG00000003743	4 retrocopies	retro_mdom_1519, retro_mdom_1520, retro_mdom_1955, retro_mdom_1956,
Mus musculus	ENSMUSG00000020719	1 retrocopy	retro_mmus_788,
Pteropus vampyrus	ENSPVAG00000001932	1 retrocopy	retro_pvam_1267,
Rattus norvegicus	ENSRNOG00000030680	1 retrocopy	retro_rnor_1277,
Tupaia belangeri	ENSTBEG00000009490	1 retrocopy	retro_tbel_4260,
Tarsius syrichta	ENSTSYG00000012149	1 retrocopy	retro_tsyr_1269,
Tursiops truncatus	ENSTTRG00000008793	1 retrocopy	retro_ttru_1662 ,