RetrogeneDB ID: retro_ttru_1095

Retrocopy location

• Organism: Dolphin (Tursiops truncatus)
• Coordinates: scaffold_102782:82087..82820(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSTTRG00000002365
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: PCBP3
• Ensembl ID: ENSTTRG00000015075
• Aliases: None
• Description: poly(rC) binding protein 3 [Source:HGNC Symbol;Acc:8651]

Sequence

>retro_ttru_1095
GTGACTGAAAGTGGACTAAATGTGACTCTCACCATTCGGCTGCTTTATGCACGGAAAGGAAGTAGGAAGCATCATTGGGA
AGAAAGGGGAGTCGGTTAAGAGGATCCGCGAGGAGAGTGGCGCGCGGATCAACATCTCGGAGGGGAATTGCCCGGAGAGA
ATCATCACTCTGACCGGCCCCACCAATGCCATCTTTAAGGCCTTCGCTATGATTATCGACAAGCTGGAAGAAGATATCAA
CAGCTCCATGACCAACAGCACGGCGGCCAGCAGGCCCCCGGTCACCCTGAGGCTGGTGGTGCCGGCCACCCAGTGCGGCT
CCCTGATTGGGAAAGGCGGGTGTAAGATCAAAGAGATCCGCGAGAGTACCGGGGCCCAGGTCCAGGTGGCGGGGGATATG
CTGCCCAACTCCACCGAGCGGGCCATCACCATTGCTGGCGTGCCGCAGTCTGTCACCGAGTGTGTCAAGCAGATCTGCCT
GGTCATGCTGGAGACGCTCTCCCAGTCTCCGCAAGGGAGAGTCATGACCATTCCGTACCAGCCCATGCCGGCCAGCTCTC
CAGTGATCTGCGCGGGCGGTCAAGATCGGTGCAGCGACGCTGCTGGCTACCCTCACGCCACCCATGACCTGGAGGGACCA
CCTCTAGATGCCTACTCGATTCAAGGACAACACACCATTTCTCCGCTCGATCTGGCCAAGCTGAACCAGGTGGCAAGACA
ACAGTCTCACTTT

Alignment

ORF - retro_ttru_1095 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 71.14 %
• Parental protein coverage: 66.48 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  VSEGGLNVTLTIRLL-MHGKEVGSIIGKKGETVKKMREESGARINISEGNCPERIVTITGPTDAIFKAFA
          V.E.GLNVTLTIRLL.MHGKEVGSIIGKKGE.VK..REESGARINISEGNCPERI.T.TGPT.AIFKAFA
Retrocopy VTESGLNVTLTIRLL>MHGKEVGSIIGKKGESVKRIREESGARINISEGNCPERIITLTGPTNAIFKAFA

Parental  MIAYKFEEDIINCMTNSPATSKPPVTLRLVVPASQCGSLIGKGGSKIKEIRESTGAQVQVAGDMLPNSTE
          MI..K.EEDI...MTNS.A.S.PPVTLRLVVPA.QCGSLIGKGG.KIKEIRESTGAQVQVAGDMLPNSTE
Retrocopy MIIDKLEEDINSSMTNSTAASRPPVTLRLVVPATQCGSLIGKGGCKIKEIRESTGAQVQVAGDMLPNSTE

Parental  RAVTISGTPDAIIQCVKQICVVMLES---PPKG--ATIPYRPKPASTPVIFAGGQVRAEPLSASTANLSL
          RA.TI.G.P.....CVKQIC.VMLE.....P.G...TIPY.P.PAS.PVI.AGGQ.R.....A.......
Retrocopy RAITIAGVPQSVTECVKQICLVMLETLSQSPQGRVMTIPYQPMPASSPVICAGGQDRCSD-AAGYPHATH

Parental  LLQPPPLPAYTIQGQYAIPHPDLTKLHQPAMQQTPF
          .L..PPL.AY.IQGQ..I...DL.KL.Q.A.QQ..F
Retrocopy DLEGPPLDAYSIQGQHTISPLDLAKLNQVARQQSHF

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_1095 retrocopy.

TSS

Tursiops truncatus was not studied using FANTOM5 data.

Lab

retro_ttru_1095 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 17 retrocopies.

Species	Parental gene accession	Retrocopies number
Cavia porcellus	ENSCPOG00000003648	1 retrocopy	retro_cpor_257,
Dipodomys ordii	ENSDORG00000003640	2 retrocopies	retro_dord_742, retro_dord_748,
Myotis lucifugus	ENSMLUG00000003074	1 retrocopy	retro_mluc_574,
Nomascus leucogenys	ENSNLEG00000002639	1 retrocopy	retro_nleu_2044,
Oryctolagus cuniculus	ENSOCUG00000002696	1 retrocopy	retro_ocun_1257,
Rattus norvegicus	ENSRNOG00000001245	1 retrocopy	retro_rnor_2656,
Sorex araneus	ENSSARG00000007629	1 retrocopy	retro_sara_414,
Tursiops truncatus	ENSTTRG00000004906	1 retrocopy	retro_ttru_1622,
Tursiops truncatus	ENSTTRG00000015075	1 retrocopy	retro_ttru_1095 ,
Tursiops truncatus	ENSTTRG00000016693	7 retrocopies	retro_ttru_1144, retro_ttru_180, retro_ttru_1922, retro_ttru_444, retro_ttru_813, retro_ttru_930, retro_ttru_937,