RetrogeneDB ID: retro_ttru_1078

Retrocopy location

• Organism: Dolphin (Tursiops truncatus)
• Coordinates: scaffold_102198:131700..132759(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: SSX2IP
• Ensembl ID: ENSTTRG00000008402
• Aliases: None
• Description: synovial sarcoma, X breakpoint 2 interacting protein [Source:HGNC Symbol;Acc:16509]

Sequence

>retro_ttru_1078
AATTCTCTTGAATATTGTCAGAAACAAATCTTAATGGAAAATGCTGAGCTTAAGAAAGTTTTTCAGCAAATGAAAAAGGA
AATAATTTCTCTTCTTTCTCCCCAAAAGCAGAAACCTAGAGAAAGAGCAGATGATAGTACAGGAACTGTTATCCCTGATA
CTGAAGATGCTGGGGAACTGAATAGAGAGAGTACGTTTCACCTTTCCTGTGCAACTGTGAGAGAGCAGCTTACCAATAGC
ATCAGAAAACAGTAGAGAATTTTGAAAAGTCACGTAGAAAAACTTGATAACCAAGTTTCAAAGGTACACCTAGAAGGTTT
TAATGATGAAGATGTAATCTCACGACAAGACCACGAACAAGAAACTGAAAAACTTGAGTTAGAAATTCAACAGCGTAAAG
AAATTATTAAAACTCGGCAGCAACTTTTACAGCAGCAGCTCGCTACTGCATGTGATGATGACACCACTTCACTGCTACAA
GACTGTTACTTGTTGGAAGAAAAGGAACGCCTCAAAGAAGAACGGTCCCTATTTAAAGAGCAAAAGAAGAATTTCGAGAA
AGAAAGACTAAGCTTTACAGAAGCAGCTATTCGCCTAGGATTGGAGAGAAAGGCATTTGAAGAAGAAAGAGCCAGTTGGG
TAAATCAACAGTTTTTAAATATGACTACCTAGGACCACCAGAGCTCAGAAAATGTGAAACTTTTCAGTGCGTTCTCAGGA
AGTTCGGATTGGGACAACCCTACAGTACACTCGAGGCCACGGCAAAAGAAACCTCACGGTGTGCCTACTGGGTCTCCACT
TAGCAAGTCTAAACTTATTAAATCTCTTCCTGCTTCTCCTTCTACTTCCGACTTTTGCCAGACACGTGCCTGTGTATCTG
AACATAGTTCAATCAATGTACTAAATATAACCCCTGAAGAATCTAAGCCATATCAAGTTGGAAGAGAATGTACAAATCAG
AAGTGGAGCGTGGTATCAAGGTCTGGATCACCGGAAGTTTGCTGTAATGGATGCTCCTCGACCCACGCAAACGCTCATGT
AGAGAAGGATGACTTACCT

Alignment

ORF - retro_ttru_1078 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 87.57 %
• Parental protein coverage: 57.59 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  NDYEYRQKQILMENAELKKVLQQMKKEMISLLSPQKQKPRERADDSTGTVISDIEEDAGELSRESTWDLS
          N..EY.QKQILMENAELKKV.QQMKKE.ISLLSPQKQKPRERADDSTGTVI.D.E.DAGEL.REST..LS
Retrocopy NSLEYCQKQILMENAELKKVFQQMKKEIISLLSPQKQKPRERADDSTGTVIPDTE-DAGELNRESTFHLS

Parental  CETVREQLTNSIRKQWRILKSHVEKLDNQVSKVHLEGFNDEDVISRQDHEQETEKLELEIQQCKEMIKTQ
          C.TVREQLTNSIRKQ.RILKSHVEKLDNQVSKVHLEGFNDEDVISRQDHEQETEKLELEIQQ.KE.IKT.
Retrocopy CATVREQLTNSIRKQ*RILKSHVEKLDNQVSKVHLEGFNDEDVISRQDHEQETEKLELEIQQRKEIIKTR

Parental  QQLLQQQLAT-CDDDTTSLLRDCYLLEEKERLKEEWSLFKEQKKNFEKERRSFTEAAIRLGLERKAFEEE
          QQLLQQQLAT.CDDDTTSLL.DCYLLEEKERLKEE.SLFKEQKKNFEKER.SFTEAAIRLGLERKAFEEE
Retrocopy QQLLQQQLATACDDDTTSLLQDCYLLEEKERLKEERSLFKEQKKNFEKERLSFTEAAIRLGLERKAFEEE

Parental  RASWLKQQFLNMTTFDHQNSENVKLFSAFSGSSDRDNPTVHSRPRQKKPHGAPSGSPVCTSKLTKSLPAS
          RASW..QQFLNMTT.DHQ.SENVKLFSAFSGSSD.DNPTVHSRPRQKKPHG.P.GSP...SKL.KSLPAS
Retrocopy RASWVNQQFLNMTT*DHQSSENVKLFSAFSGSSDWDNPTVHSRPRQKKPHGVPTGSPLSKSKLIKSLPAS

Parental  PSTSDFCQTRSCVSEYSSISVLNTTPEESKPNQVGRECTNQKWSVASRTDSQEACCSGCSSTHADAHIEK
          PSTSDFCQTR.CVSE.SSI.VLN.TPEESKP.QVGRECTNQKWSV.SR..S.E.CC.GCSSTHA.AH.EK
Retrocopy PSTSDFCQTRACVSEHSSINVLNITPEESKPYQVGRECTNQKWSVVSRSGSPEVCCNGCSSTHANAHVEK

Parental  DDLP
          DDLP
Retrocopy DDLP

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_1078 retrocopy.

TSS

Tursiops truncatus was not studied using FANTOM5 data.

Lab

retro_ttru_1078 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 5 retrocopies.

Species	Parental gene accession	Retrocopies number
Homo sapiens	ENSG00000117155	1 retrocopy	retro_hsap_2822,
Pongo abelii	ENSPPYG00000001201	1 retrocopy	retro_pabe_2206,
Pan troglodytes	ENSPTRG00000000906	1 retrocopy	retro_ptro_1913,
Tarsius syrichta	ENSTSYG00000004276	1 retrocopy	retro_tsyr_526,
Tursiops truncatus	ENSTTRG00000008402	1 retrocopy	retro_ttru_1078 ,