RetrogeneDB ID: retro_ttru_994

Retrocopy location

• Organism: Dolphin (Tursiops truncatus)
• Coordinates: GeneScaffold_922:467117..468212(+)
• Located in intron of: ENSTTRG00000013165

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSTTRG00000016157
• Aliases: None
• Description: None

Sequence

>retro_ttru_994
ATGAAGATCGAGGAAGCCAAGAAACCCTCTTTCCCATGGTGTGGCATGGACATCGGGGGAACTCTGGTAAAGCGCTCATA
TTTTGAACCTATCGATATCACAGCAGAGGAAGAAGAAGTTGAGAGCTTAAAAAGTATCCGGAAATACGTGACTTCTAATG
TAGCCTATGGATCCACTGGTATTCAGGATGTACGCCTTGAACTGAAAGATTTAACACTTTTTGGCTGGACGGGGAACTTG
CACTTTATCAGATTTCCAACCCAGGACCTGCCTACTTTTATCCAAAGGGGAAGAGATAAAACCTTCTCAACATTACACAC
GGTGCTATGTGCTACAGGAGGTGGTGCTGACAAGTCTGAAAACGATTTTCACACAGTTGGAAACCCCCACCTGCACAAAC
TGGATGAACCTGACTGCCTTGTAAAGGGCTTGCTGTAGACAGATTCTGTCAGTTTCAGTGGACAAGCAGAGTGCTATTAT
TTTGCTAATGCCTCAGAACCTGAGAGATGCCAAAAGATGCCTTTCAACCTGGATGATCCCTATCCACTTCTGGTAGTAAA
CACTGGTTCCCAGTCAGTATTTTAGCAGTCCATTCCAAAGACAACTATGAACAAGTAACTGGGACAAGCCTTGGAGGGGC
TACCTTTCTGGGTTTATGTAGTTTATTGACTGGCTGTGAAAGTTTTGAAGAGGCTCTTGAAATGGCATCCAAAGGTGACA
GCACCCAAGCTGACAAGCTGGTCCCTGATATTTACAGAGGAGATATGAAAGATTTGGTCTGCCTGGCTGGGCTGCAGCGT
CTAGTTTTGGGAATATGATTTAGAAGGAGAGGCGAGAATCTGTTAGTAAACAGCATCTAGCAAGAGCTACATTAGTTACC
ATCACCAATAACATGGGTTCTGTGGCACGAATGTGGGCTGTTAATGAGAAAATAAACAGTTGTCTTTGTTGGAAACTTTA
CGTGTCACTACTCTCGATAAAACTCTTGGCATATGCACTGGATTACTGTCAAAAGGTCAACTGAAAGCATTGTTTCTAGA
GCATGAGGGGTATTCTGGAGCAGTTGGTACACTTCTTGGGCTGCCAAATTTCAGC

Alignment

ORF - retro_ttru_994 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 83.65 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 2
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  MKIKDAKKPSFPWFGMDIGGTLVKLSYFEPIDITAEEEQEEVESLKSIRKYLTSNVAYGSTGIRDVHLEL
          MKI..AKKPSFPW.GMDIGGTLVK.SYFEPIDITAEEE..EVESLKSIRKY.TSNVAYGSTGI.DV.LEL
Retrocopy MKIEEAKKPSFPWCGMDIGGTLVKRSYFEPIDITAEEE--EVESLKSIRKYVTSNVAYGSTGIQDVRLEL

Parental  KDLTLFGRRGNLHFIRFPTQDLPTFIQMGRDKNFSTLHTVLCATGGGAYKFEKDFRTIGNLHLHKLDELD
          KDLTLFG..GNLHFIRFPTQDLPTFIQ.GRDK.FSTLHTVLCATGGGA.K.E.DF.T.GN.HLHKLDE.D
Retrocopy KDLTLFGWTGNLHFIRFPTQDLPTFIQRGRDKTFSTLHTVLCATGGGADKSENDFHTVGNPHLHKLDEPD

Parental  CLVKGLLYIDSVSFNGQAECYYFANASEPERCQKMPFNLDDPYPLLVVNIGS-GVSILAVHSKDNYKRVT
          CLVKGLL..DSVSF.GQAECYYFANASEPERCQKMPFNLDDPYPLLVVN.GS..VSILAVHSKDNY..VT
Retrocopy CLVKGLL*TDSVSFSGQAECYYFANASEPERCQKMPFNLDDPYPLLVVNTGS<PVSILAVHSKDNYEQVT

Parental  GTSLGGGTFLGLCSLLTGCESFEEALEMASKGDSTQADKLVRDIYGGD-YERFGLPGWAVASSFGNMIYK
          GTSLGG.TFLGLCSLLTGCESFEEALEMASKGDSTQADKLV.DIY.GD.YERFGLPGWA.ASSFGNMI.K
Retrocopy GTSLGGATFLGLCSLLTGCESFEEALEMASKGDSTQADKLVPDIYRGD<YERFGLPGWAAASSFGNMI*K

Parental  EKRESVSKEDLARATLVTITNNIGSVARMCAVNEKINRVVFVGNFLRVNTLSMKLLAYALDY-WSKGQLK
          E.RESVSK..LARATLVTITNN.GSVARM.AVNEKIN..................LAYALDY..SKGQLK
Retrocopy ERRESVSKQHLARATLVTITNNMGSVARMWAVNEKINSCLCWKLYVSLLSIKL--LAYALDY<LSKGQLK

Parental  ALFLEHEGYFGAVGALLGLPNFS
          ALFLEHEGY.GAVG.LLGLPNFS
Retrocopy ALFLEHEGYSGAVGTLLGLPNFS

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_994 retrocopy.

TSS

Tursiops truncatus was not studied using FANTOM5 data.

Lab

retro_ttru_994 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 17 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000011633	4 retrocopies	retro_chof_1188, retro_chof_1391, retro_chof_1837, retro_chof_830,
Callithrix jacchus	ENSCJAG00000015550	1 retrocopy	retro_cjac_2037,
Homo sapiens	ENSG00000120137	1 retrocopy	retro_hsap_779,
Gorilla gorilla	ENSGGOG00000004947	1 retrocopy	retro_ggor_646,
Nomascus leucogenys	ENSNLEG00000004896	5 retrocopies	retro_nleu_1430, retro_nleu_144, retro_nleu_2975, retro_nleu_3058, retro_nleu_3099,
Pongo abelii	ENSPPYG00000016024	1 retrocopy	retro_pabe_2848,
Pan troglodytes	ENSPTRG00000017509	1 retrocopy	retro_ptro_608,
Tursiops truncatus	ENSTTRG00000016157	3 retrocopies	retro_ttru_1947, retro_ttru_29, retro_ttru_994 ,