RetrogeneDB ID: retro_ttru_1726

Retrocopy location

• Organism: Dolphin (Tursiops truncatus)
• Coordinates: scaffold_88745:9126..9944(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSTTRG00000008940
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: COQ2
• Ensembl ID: ENSTTRG00000005647
• Aliases: None
• Description: coenzyme Q2 4-hydroxybenzoate polyprenyltransferase [Source:HGNC Symbol;Acc:25223]

Sequence

>retro_ttru_1726
TTGGCAGCCCAACCAGGCTGTTTTCCGGATTGGTACGTGTTATCTTCTCTCTGGCACTGGAGCTGTTCTGCTGCGTGAAG
CAGGCTGTACTATTAATGACATGTGGGACCAGGACTATGATAAAAAGGTTCCAGGAACAGCAAGTCACCCAATAGCTGCT
GGAGACATTTCAACTTTTCAATCCTTTGTTTTTCTTGGGGGACAGCTGACCTTGGCACTGCGTGTTCTTCTGTGTCTGAA
TTACTACAGTATAGCTCTCGGAGCAGCATCCCTACTTCTTGTCATCACCTACCCGCTAATGAAGAGAATTACACACTGGC
CTCAATTAGCCTTGGGGGTGACTTTTAATCGGGGAGCATTACTTGGATGGTCTGCTATCAAGGGCTCCTGTGATCCATCT
GTTTGCCTCCCTCTTTATTTTTCTGGGATTATGTGCACTCATATACGATACTATCTATGCTCATCAGGACAAGAGAGATG
ATGCTCGGATCGGGTTTAAGTCCACGGCACTGCTGTTCCGTGAAGATACCAAGCAGTGGCTCAGTGGCTTCACTGTGGCG
ATGCTGGGGCCACTGAGCCTGCTGGGAGTGAACGTCGGTCAAACTGTGCCCTACTACACTGCTGTGGTTGTTGTAGGAGC
CCATCTGGCTCACCAGATTTACACTCTGGACATCCACAGACCTGAGGATTGTTGGGATAAATTCACCTCCAACCGAACAA
TAGGACTAATACTTTTTTTAGGGATTGTCCTTGGGAATTTGTGGAAAGAAAAGGAGACAGATGAAACAAAGAAAAATACA
GATAATAGAACGGAAAAT

Alignment

ORF - retro_ttru_1726 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 84.36 %
• Parental protein coverage: 66.5 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  LAAEPGCFPDWYMLS-LFGTGAVLMRGAGCTINDMWDQDYDKKVTRTASRPIAAGDISTFQSFVFLGGQL
          LAA.PGCFPDWY.LS.L.GTGAVL.R.AGCTINDMWDQDYDKKV..TAS.PIAAGDISTFQSFVFLGGQL
Retrocopy LAAQPGCFPDWYVLS>LSGTGAVLLREAGCTINDMWDQDYDKKVPGTASHPIAAGDISTFQSFVFLGGQL

Parental  TLALGVLLCLNYYSIALGAASLLLVITYPLMKRITYWPQLALGLTFNWGALLGWSAVKGSCDPSVCLPLY
          TLAL.VLLCLNYYSIALGAASLLLVITYPLMKRIT.WPQLALG.TFN.GALLGWSA.KGSCDPSVCLPLY
Retrocopy TLALRVLLCLNYYSIALGAASLLLVITYPLMKRITHWPQLALGVTFNRGALLGWSAIKGSCDPSVCLPLY

Parental  -FSGIMWTLIYDTIYAHQDKRDDALIGLKSTALLFREDTKQWLSGFTVAMLGALSLLGV-IDQTVPYYXX
          .F.G....LIYDTIYAHQDKRDDA.IG.KSTALLFREDTKQWLSGFTVAMLG.LSLLGV...QTVPYY..
Retrocopy >FLGLC-ALIYDTIYAHQDKRDDARIGFKSTALLFREDTKQWLSGFTVAMLGPLSLLGVNVGQTVPYYTA

Parental  XXXXXXXXXXXIYTLDIHRPEDCWDKFTSNRTIGLIIFLGIVLGNLWKEKETDKTKKNIDNRVEN
          ...........IYTLDIHRPEDCWDKFTSNRTIGLI.FLGIVLGNLWKEKETD.TKKN.DNR.EN
Retrocopy VVVVGAHLAHQIYTLDIHRPEDCWDKFTSNRTIGLILFLGIVLGNLWKEKETDETKKNTDNRTEN

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_1726 retrocopy.

TSS

Tursiops truncatus was not studied using FANTOM5 data.

Lab

retro_ttru_1726 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 8 parental genes, and 37 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000005006	1 retrocopy	retro_amel_1898,
Bos taurus	ENSBTAG00000005744	1 retrocopy	retro_btau_1835,
Cavia porcellus	ENSCPOG00000011458	1 retrocopy	retro_cpor_1202,
Equus caballus	ENSECAG00000012542	1 retrocopy	retro_ecab_432,
Myotis lucifugus	ENSMLUG00000015267	1 retrocopy	retro_mluc_1776,
Mus musculus	ENSMUSG00000029319	1 retrocopy	retro_mmus_2883,
Tarsius syrichta	ENSTSYG00000013801	30 retrocopies	retro_tsyr_1015, retro_tsyr_1155, retro_tsyr_1173, retro_tsyr_1180, retro_tsyr_1207, retro_tsyr_1235, retro_tsyr_1327, retro_tsyr_1335, retro_tsyr_1385, retro_tsyr_1451, retro_tsyr_1491, retro_tsyr_1646, retro_tsyr_1709, retro_tsyr_1742, retro_tsyr_2015, retro_tsyr_2062, retro_tsyr_2087, retro_tsyr_2136, retro_tsyr_2146, retro_tsyr_466, retro_tsyr_513, retro_tsyr_533, retro_tsyr_54, retro_tsyr_548, retro_tsyr_607, retro_tsyr_619, retro_tsyr_654, retro_tsyr_776, retro_tsyr_839, retro_tsyr_995,
Tursiops truncatus	ENSTTRG00000005647	1 retrocopy	retro_ttru_1726 ,