RetrogeneDB ID: retro_ttru_236

Retrocopy location

• Organism: Dolphin (Tursiops truncatus)
• Coordinates: GeneScaffold_1635:866936..867902(-)
• Located in intron of: ENSTTRG00000007157

Retrocopy information

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

Parental gene information

• Parental gene symbol: PRPF38B
• Ensembl ID: ENSTTRG00000006479
• Aliases: None
• Description: PRP38 pre-mRNA processing factor 38 (yeast) domain containing B [Source:HGNC Symbol;Acc:25512]

Sequence

>retro_ttru_236
GAGGTCACACATGTTGAACCATGGGAGAAAGGAAGCAGGAAAACAGCTGGCCAAACAGGGATGTGCAGAGGGGTTCAAGG
TGTTGGGACAGGAGGAATTGTTTCTACAGCTTTTTGCCTGTTATACAAATTATTTACTCTGAAGTTAACTCGCAAGCAAG
TGATGGGTCTTATAACACACACAGACTCTCCATATATTAGAGCCCTTGGATTTATGTATATAAGGTACACACAGCCCCCT
ACAGATCTATGGGATTGGTTTGAATCCTTCCTTCATGATGAAGAGGACCTAGATGTGAAGGCTGGTGGAGGCTGCGTAAT
GACCATTGGAGAAATGCTACGGTCTTTTCTCACAAAACTGGAGTGGTTTTCCACTTTGTTTCCAAGAATTCCAGTTCCAG
TTCAGAAGAATATTGATCAACAGATTAAAACCTGACCAAGAAAAATCAAGAAAGATGGAAAGGAAAGCGCTGAGGAAATA
GACAGACATGTTGAACGCAGGCGTTCAAGGTCTCCAAGGAGATCACTGAGTCCACGGAGGTCCCCAAGAAGATCCAGAAG
TAGAAGCCATCATCGGGAGGGCCATGGGTCTTCTAGTTTTGACCGAGAATTAGAAAGAGAGAAAGAACGCCAGCGACTAG
AGCGTGAAGCCAAAGAAAGGGAAAAAGAAAGGCGAAGATCCCGAAGTATTGATCGGGGGCTAGAACGCAGGCATAGCAGG
AGTAGGGAAAGACATAGAAGCCGTATTCGAAGTCGTGATAGGAAAGGGGATAGAAGGGACAGGGATCGGGAAAGAGAGAA
AGAAAATGAGAGAGGTAGAAGACGAGATCGTGACTATGATAAGGAAAGAGGTAATGACTGAGAAAAGGAGAGGTCAAGAG
AACGGTCCAAGGAACGGAGAAGTAGGGGTGAGGTAGAAGAAAAGAAATATAAAGAAGACAAAGATGATAGGCGGCATAGA
GATGAC

Alignment

ORF - retro_ttru_236 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 97.83 %
• Parental protein coverage: 59.19 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  KVTHVEPWEKGSRKTAGQTGMCGGVRGVGTGGIVSTAFCLLYKLFTLKLTRKQVMGLITHTDSPYIRALG
          .VTHVEPWEKGSRKTAGQTGMC.GV.GVGTGGIVSTAFCLLYKLFTLKLTRKQVMGLITHTDSPYIRALG
Retrocopy EVTHVEPWEKGSRKTAGQTGMCRGVQGVGTGGIVSTAFCLLYKLFTLKLTRKQVMGLITHTDSPYIRALG

Parental  FMYIRYTQPPTDLWDWFESFLDDEEDLDVKAGGGCVMTIGEMLRSFLTKLEWFSTLFPRIPVPVQKNIDQ
          FMYIRYTQPPTDLWDWFESFL.DEEDLDVKAGGGCVMTIGEMLRSFLTKLEWFSTLFPRIPVPVQKNIDQ
Retrocopy FMYIRYTQPPTDLWDWFESFLHDEEDLDVKAGGGCVMTIGEMLRSFLTKLEWFSTLFPRIPVPVQKNIDQ

Parental  QIKTRPRKIKKDGKESAEEIDRHVERRRSRSPRRSLSPRRSPRRSRSRSHHREGHGSSSFDRELEREKER
          QIKT.PRKIKKDGKESAEEIDRHVERRRSRSPRRSLSPRRSPRRSRSRSHHREGHGSSSFDRELEREKER
Retrocopy QIKT*PRKIKKDGKESAEEIDRHVERRRSRSPRRSLSPRRSPRRSRSRSHHREGHGSSSFDRELEREKER

Parental  QRLEREAKEREKERRRSRSIDRGLERRHSRSRERHRSRSRSRDRKGDRRDRDREREKENERGRRRDRDYD
          QRLEREAKEREKERRRSRSIDRGLERRHSRSRERHRSR.RSRDRKGDRRDRDREREKENERGRRRDRDYD
Retrocopy QRLEREAKEREKERRRSRSIDRGLERRHSRSRERHRSRIRSRDRKGDRRDRDREREKENERGRRRDRDYD

Parental  KERGNDREKERSRERSKERRSRGEVEEKKYKEDKDDRRHRDD
          KERGND.EKERSRERSKERRSRGEVEEKKYKEDKDDRRHRDD
Retrocopy KERGND*EKERSRERSKERRSRGEVEEKKYKEDKDDRRHRDD

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_236 retrocopy.

TSS

Tursiops truncatus was not studied using FANTOM5 data.

Lab

retro_ttru_236 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	ENSCJAG00000002510	1 retrocopy	retro_cjac_3189,
Nomascus leucogenys	ENSNLEG00000001645	1 retrocopy	retro_nleu_350,
Tursiops truncatus	ENSTTRG00000006479	1 retrocopy	retro_ttru_236 ,