RetrogeneDB ID: retro_ttru_1355

Retrocopy location

• Organism: Dolphin (Tursiops truncatus)
• Coordinates: scaffold_111332:106695..107415(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: GPBP1L1
• Ensembl ID: ENSTTRG00000012202
• Aliases: None
• Description: GC-rich promoter binding protein 1-like 1 [Source:HGNC Symbol;Acc:28843]

Sequence

>retro_ttru_1355
ATGGTGCAGCATGACTTTGTTCCTGCTTGACTAAATTTCTCAGCACCACAGTCAGCTAAGTCACCTACAGCCACCTTTGA
AAAACACGGAGAGCACCTACCCTGAGGAGGTGGTAGACTTGGAGTAAGCCGTCGTCGACCTAATTCCTCTGATGGCTTTT
TTTAACAATGGACCTCTACGAACGACAGGAGATTCCTGGCACCAGCCCTCCCTATTCCGCCATGATTCCGTGGACTCTGG
TGTCTCTAAGGGAGCATATGCTGGAATCACAGGGAACCTATCTGGTTGGCACGGCTCTTCCCGAGGTCACGACGGCATGA
GCCAGCGTAGTGGGGTGGCACAGGGAACCATCACCACTGGAATGGCAGCTTCCACTCCCGGAAAGGCTGTGCCTTTCAGG
AAAAGCCAGCTACAGAGATTAGGGCAGAGAAGAAAGATGATAAGGTGGAAGGGTTGCAGTTTGAAGAAGACGACTTTCCT
TCTTTGAATCCAGAACCTGACAAACAGAGTCAGCCATGTAGACCTATGGGAACCCCTTCTGGACTGTGGGAAAACCCACC
TAGTGCCAAGCAGCCCTCCAAAATGCTAGGCATCAAAAAAGTTTCCAAACAAGATCCTGCTGCTGCCTTCTCTGCTGCAT
TCACCTCACCAGGATCTCACCATGCAAAATGAAAACAAATTGTCACCCGTGGGTTCCCAAGTGTCTATAAGACCCGGGTT

Alignment

ORF - retro_ttru_1355 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 88.52 %
• Parental protein coverage: 50.42 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 5

Retrocopy - Parental Gene Alignment:

Parental  MAQHDFVPAWLNFSTPQSAKSPTATFEKHGEHLPRGDGRFGVSRRRHNSSDGFF-NNGPLRTTGDSWHQP
          M.QHDFVPA.LNFS.PQSAKSPTATFEKHGEHLP.G.GR.GVSRRR.NSSDGFF.NNGPLRTTGDSWHQP
Retrocopy MVQHDFVPA*LNFSAPQSAKSPTATFEKHGEHLP*GGGRLGVSRRRPNSSDGFF>NNGPLRTTGDSWHQP

Parental  SLFRHDSVDSGVSKGAYAGITGNLSGWHGSSRGHDGMSQRSG-GGTGNHRHWNGSFHSRKGCAFQEKPPT
          SLFRHDSVDSGVSKGAYAGITGNLSGWHGSSRGHDGMSQRSG.GGTGNH.HWNGSFHSRKGCAFQEKP.T
Retrocopy SLFRHDSVDSGVSKGAYAGITGNLSGWHGSSRGHDGMSQRSG<GGTGNHHHWNGSFHSRKGCAFQEKPAT

Parental  EIREEKKDDKVEKLQFEEDDFPSLNPEAGKQNQPCRPIGTPSGVWENPPSAKQPSKMLVIKKVSKEDPAA
          EIR.EKKDDKVE.LQFEEDDFPSLNPE..KQ.QPCRP.GTPSG.WENPPSAKQPSKML.IKKVSK.DPAA
Retrocopy EIRAEKKDDKVEGLQFEEDDFPSLNPEPDKQSQPCRPMGTPSGLWENPPSAKQPSKMLGIKKVSKQDPAA

Parental  AFSAAFTSPGSHHA-NGNKLSTM-VP-SVYKNLV
          AFSAAFTSPGSHHA.N.NKLS...VP.SVYK..V
Retrocopy AFSAAFTSPGSHHA>NENKLSPV>VP>SVYKTRV

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_1355 retrocopy.

TSS

Tursiops truncatus was not studied using FANTOM5 data.

Lab

retro_ttru_1355 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 5 parental genes, and 6 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000010454	1 retrocopy	retro_chof_53,
Myotis lucifugus	ENSMLUG00000012432	2 retrocopies	retro_mluc_211, retro_mluc_834,
Rattus norvegicus	ENSRNOG00000037595	1 retrocopy	retro_rnor_390,
Sorex araneus	ENSSARG00000004852	1 retrocopy	retro_sara_242,
Tursiops truncatus	ENSTTRG00000012202	1 retrocopy	retro_ttru_1355 ,