RetrogeneDB ID: retro_ttru_237

Retrocopy location

• Organism: Dolphin (Tursiops truncatus)
• Coordinates: GeneScaffold_1635:918323..919841(-)
• Located in intron of: ENSTTRG00000007157

Retrocopy information

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

Parental gene information

• Parental gene symbol: DYNC1I2
• Ensembl ID: ENSTTRG00000011355
• Aliases: None
• Description: dynein, cytoplasmic 1, intermediate chain 2 [Source:HGNC Symbol;Acc:2964]

Sequence

>retro_ttru_237
CGAGGACCTATTAAACTTGGAATGGCTAAAATTACACAAGTTGACTTTCCTCCTCGTGAAATCGTCACATATACGAAGGA
AACTCAGACTCCAGTTATGGCTCAACCCAAAGAAGATGAAGAGGAAGAAGATGACGTAGTGACTCCTAAACCACCTATTG
AACCTGAGGAAGAGAAAACTTTAAAGAAAGATGAAGAAAGTGATAGTAAAGCCCCCCCGCACGAGCTGACTGAAGAAGAA
AAGCAGCAAATCTTGCACTCTGAGGAATTTTTAAGTTTCTTCGACCATTCTACAAGAATTGTAGAAAGAGCTCTTTCTGA
GCAGATTAACATCTTCTTTGACTACAGTGGAAGAGATTTGGAAGACAAAGAAGGAGAGATTCAAGCAGGTGCTAAACTGT
CATTAAATCGACAATTTTTTGACGAACGTTGGTCAAAGCATCGGGTTGTTAGTTGTTTGGATTGGTCATCTCAGTATCCA
GAGTTACTTGTGGCTTCCTATAATAACAACGAAGATGCTCCTCATGAGCCTGATGGTGTGGCCCTTGTATGGAATATGAA
ATACAAAAAAACTACTCCAGAGTATGTGTTTCACTGCCAGTCAGCCGTTATGTCTGCTACATTTGCAAAATTTCATCCAA
ATCTGGTTGTTGGTGGTACATATTCAGGCCAGACTGTGCTGTGGGATAACCGTAGCAATAAAAGAACTCCAGTGCAAAGA
ACTCCAATGTCAGCTGCAGCACACACACATCCTGTATATTGTGTAAATGTTGTTGGGACACAGAACGCTCACAATCTGAT
TAGTATCTCTACTGATGGAAAAATTTGTTCGTGGAGTCTGGACATGCTTTCCCATCCACAGGATAGCATGGAATTGGTTC
ATAAACAGTCAAAGGCAGTCGCTGTGACATCTATGTCCTTCCCTGTTGGAGATGTCAACAACTTCGTTGTTGGGAGTGAA
GAAGGTTCTGTGTACACAGCATGCCGCCATGGCAGCAAAGCTGGAATCAGTGAGATGTTCGAGGGACATCAAGGACCAAT
TACTGGCATTCATTGTCATGCAGCTGTTGGAGCAGTGGACTTCTCACATCTTTTTGTCACTTCATCATTTGACTGGACAG
TAAAACTTTGGACAACTAAGAATAACAAGCCTTTGTACTCATTTGAAGATAATTCAGACTATGTTTATGATGTTATGTGG
TCACCCACCCACCCAGCCCTGTTTGCCTGTGTGGATGGCATGGGTAGGCTGGATTTGTGGAATCTCAATAATGACACAGA
GGTGCCAACTGCCAGCATTTCTGTGGAGGGTAATCCTGCTCTTAATCGTGTAAGATGGACCCATTCTGGAAGAGAGATTG
CCGTGGGTGATTCTGAAGGACAGATTGTTATATATGATGTGGGAGAGCAGATTGCTGTCCCCCGAAATGATGAATGGGCA
CGGTTTGGCCGAACACTTGCAGAAATTAATGCAAACCGAGCGGATGCAGAGGAGGAAGCAGCTGCCCGAATACCTGCT

Alignment

ORF - retro_ttru_237 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 99.21 %
• Parental protein coverage: 84. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  RGPIKLGMAKITQVDFPPREIVTYTKETQTPVMAQPKEDEEEEDDVVTPKPPIEPEEEKTLKKDEESDSK
          RGPIKLGMAKITQVDFPPREIVTYTKETQTPVMAQPKEDEEEEDDVVTPKPPIEPEEEKTLKKDEESDSK
Retrocopy RGPIKLGMAKITQVDFPPREIVTYTKETQTPVMAQPKEDEEEEDDVVTPKPPIEPEEEKTLKKDEESDSK

Parental  APPHELTEEEKQQILHSEEFLSFFDHSTRIVERALSEQINIFFDYSGRDLEDKEGEIQAGAKLSLNRQFF
          APPHELTEEEKQQILHSEEFLSFFDHSTRIVERALSEQINIFFDYSGRDLEDKEGEIQAGAKLSLNRQFF
Retrocopy APPHELTEEEKQQILHSEEFLSFFDHSTRIVERALSEQINIFFDYSGRDLEDKEGEIQAGAKLSLNRQFF

Parental  DERWSKHRVVSCLDWSSQYPELLVASYNNNEDAPHEPDGVALVWNMKYKKTTPEYVFHCQSAVMSATFAK
          DERWSKHRVVSCLDWSSQYPELLVASYNNNEDAPHEPDGVALVWNMKYKKTTPEYVFHCQSAVMSATFAK
Retrocopy DERWSKHRVVSCLDWSSQYPELLVASYNNNEDAPHEPDGVALVWNMKYKKTTPEYVFHCQSAVMSATFAK

Parental  FHPNLVVGGTYSGQIVLWDNRSNKRTPVQRTPLSAAAHTHPVYCVNVVGTQNAHNLISISTDGKICSWSL
          FHPNLVVGGTYSGQ.VLWDNRSNKRTPVQRTP.SAAAHTHPVYCVNVVGTQNAHNLISISTDGKICSWSL
Retrocopy FHPNLVVGGTYSGQTVLWDNRSNKRTPVQRTPMSAAAHTHPVYCVNVVGTQNAHNLISISTDGKICSWSL

Parental  DMLSHPQDSMELVHKQSKAVAVTSMSFPVGDVNNFVVGSEEGSVYTACRHGSKAGISEMFEGHQGPITGI
          DMLSHPQDSMELVHKQSKAVAVTSMSFPVGDVNNFVVGSEEGSVYTACRHGSKAGISEMFEGHQGPITGI
Retrocopy DMLSHPQDSMELVHKQSKAVAVTSMSFPVGDVNNFVVGSEEGSVYTACRHGSKAGISEMFEGHQGPITGI

Parental  HCHAAVGAVDFSHLFVTSSFDWTVKLWTTKNNKPLYSFEDNSDYVYDVMWSPTHPALFACVDGMGRLDLW
          HCHAAVGAVDFSHLFVTSSFDWTVKLWTTKNNKPLYSFEDNSDYVYDVMWSPTHPALFACVDGMGRLDLW
Retrocopy HCHAAVGAVDFSHLFVTSSFDWTVKLWTTKNNKPLYSFEDNSDYVYDVMWSPTHPALFACVDGMGRLDLW

Parental  NLNNDTEVPTASIS-EGNPALNR-RWTHSGREIAVGDSEGQIVIYDVGEQIAVPRNDEWARFGRTLAEIN
          NLNNDTEVPTASIS.EGNPALNR.RWTHSGREIAVGDSEGQIVIYDVGEQIAVPRNDEWARFGRTLAEIN
Retrocopy NLNNDTEVPTASISVEGNPALNRVRWTHSGREIAVGDSEGQIVIYDVGEQIAVPRNDEWARFGRTLAEIN

Parental  ANRADAEEEAAARIPA
          ANRADAEEEAAARIPA
Retrocopy ANRADAEEEAAARIPA

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_237 retrocopy.

TSS

Tursiops truncatus was not studied using FANTOM5 data.

Lab

retro_ttru_237 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 3 parental genes, and 3 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000007196	1 retrocopy	retro_cjac_3204,
Homo sapiens	ENSG00000077380	1 retrocopy	retro_hsap_574,
Tursiops truncatus	ENSTTRG00000011355	1 retrocopy	retro_ttru_237 ,