RetrogeneDB ID: retro_ttru_87

Retrocopy location

• Organism: Dolphin (Tursiops truncatus)
• Coordinates: GeneScaffold_1184:37088..37970(+)
• Located in intron of: ENSTTRG00000010792

Retrocopy information

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

Parental gene information

• Parental gene symbol: OAT
• Ensembl ID: ENSTTRG00000004225
• Aliases: None
• Description: ornithine aminotransferase [Source:HGNC Symbol;Acc:8091]

Sequence

>retro_ttru_87
ACAGGAGTGGAGGCTGGAGAGAGTGCTTGCAAACTTACTCGGAGATGGGGATATACTACTGAGAAGGGTATCCCAAAGAT
TGTTTTTTGCAGCCGGAAACTTTTGGAGGTAGAACATTGTCAGCAATCTCCAGTTCCACACACCCAACCAGTTACAATGG
TTTTGGACCATTTATGTCAGGTTTTGAAATCACTCCATATAATGATCTGCCTGTCTTGAGCGTGCACTTCAGGATCCAAA
TGTTGTGGCGTTCATGGTGGAACCAACTCAGGGTGAAGCAGGCGTTGTTGTTCTGGATCCAGGCTACTTGTGGGTGTGCA
AGAGCTCTAAACCCAGCACCAGGCTCTGTTTATTGCTGATGAAATACAGACAGGATTGGCCAGAACTGGTAGATGGCTGG
CTATTGATCACGAAAATGTCAGACCTGATACAGTTCTTCTAGGAAAGGCACTTTCTGGTGGTTTATACCCTGTATCCACA
GTGTTGTATAATGATGAAATAATGTTGACCATTAAACCAGGGGAACATGGTTCTATGTACGGTGGCAATCCACTAGGCTG
CCGAGTGTCCATCACAGCCCTTGAGGTTTTGGAAGAAGAAAACCTTGCTGAAAAATGCAGACAAATGGGTATCATCTTGA
GAAATGAACGCATGAAGCTACCTTCTGATATTGTAACTGCTGTAAGAGGAAAAGGATTATTAAATGCTATTGTTATTAGA
GAAACCAAAGACTGTGATGCTTGGAAGGTATGTCTGTGACTTCGAGATAATGGACTTCTGGACAAGCCAACCCATGGTGA
TATCATCAGGTTTGCACCTCCGCTTGTGATCAAGGAGGAGGAGATTCTGGAGGCCATGGACATCATTAACAAGAACATCT
TG

Alignment

ORF - retro_ttru_87 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 82.78 %
• Parental protein coverage: 67.51 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  TGVEAGETACKLARRWGYTV-KGIPKYKAKIVF-AAGNFW-GRTLSAISSSTDPTSYDGFGPFMPGFEII
          TGVEAGE.ACKL.RRWGYT..KGIPK....IVF.AAGNFW.GRTLSAISSST.PTSY.GFGPFM.GFEI.
Retrocopy TGVEAGESACKLTRRWGYTTEKGIPK----IVF>AAGNFW>GRTLSAISSSTHPTSYNGFGPFMSGFEIT

Parental  PYNDLP-ALERALQDPNVAAFMVEPIQGEAGVVVPDPGY-LVGVRELCTQHQVLFIADEVQTGLARTGRW
          PYNDLP..LERALQDPNV.AFMVEP.QGEAGVVV.DPGY.LVGV.EL.TQHQ.LFIADE.QTGLARTGRW
Retrocopy PYNDLP<CLERALQDPNVVAFMVEPTQGEAGVVVLDPGY<LVGVQEL*TQHQALFIADEIQTGLARTGRW

Parental  LAVDHENVRPDMVLLGKALSGGLYPVSAVLCDDEIMLTIKSGEHGFTYGG-PL-CRA--IAAGVLEEENL
          LA.DHENVRPD.VLLGKALSGGLYPVS.VL..DEIMLTIK.GEHG..YGG.PL.CR....A..VLEEENL
Retrocopy LAIDHENVRPDTVLLGKALSGGLYPVSTVLYNDEIMLTIKPGEHGSMYGGNPLGCRVSITALEVLEEENL

Parental  AENAEKMGIILRNELMKLPSDIVTAVRGKGLLNAIVIRETKDYDAWKVCLRLRDNGLLAKPTHGDIIRFA
          AE....MGIILRNE.MKLPSDIVTAVRGKGLLNAIVIRETKD.DAWKVCL.LRDNGLL.KPTHGDIIRFA
Retrocopy AEKCRQMGIILRNERMKLPSDIVTAVRGKGLLNAIVIRETKDCDAWKVCL*LRDNGLLDKPTHGDIIRFA

Parental  PPLVIKEDEILEAVEIINKTIL
          PPLVIKE.EILEA..IINK.IL
Retrocopy PPLVIKEEEILEAMDIINKNIL

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_87 retrocopy.

TSS

Tursiops truncatus was not studied using FANTOM5 data.

Lab

retro_ttru_87 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 12 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000012633	1 retrocopy	retro_cjac_2462,
Homo sapiens	ENSG00000065154	1 retrocopy	retro_hsap_4828,
Gorilla gorilla	ENSGGOG00000000848	1 retrocopy	retro_ggor_3010,
Macropus eugenii	ENSMEUG00000005655	1 retrocopy	retro_meug_613,
Mus musculus	ENSMUSG00000030934	1 retrocopy	retro_mmus_3475,
Nomascus leucogenys	ENSNLEG00000000482	2 retrocopies	retro_nleu_2176, retro_nleu_503,
Pongo abelii	ENSPPYG00000002737	2 retrocopies	retro_pabe_2989, retro_pabe_3754,
Pan troglodytes	ENSPTRG00000003028	1 retrocopy	retro_ptro_3213,
Sus scrofa	ENSSSCG00000010734	1 retrocopy	retro_sscr_1181,
Tursiops truncatus	ENSTTRG00000004225	1 retrocopy	retro_ttru_87 ,