RetrogeneDB ID: retro_ttru_1154

Retrocopy location

• Organism: Dolphin (Tursiops truncatus)
• Coordinates: scaffold_105800:500237..500908(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: TXNL1
• Ensembl ID: ENSTTRG00000001161
• Aliases: None
• Description: thioredoxin-like 1 [Source:HGNC Symbol;Acc:12436]

Sequence

>retro_ttru_1154
GGAATAGCTGCCACCAACAATATGTCAGCAATACCTACATTTTTGTTTTTTTGAAACAAAGTGACAGTTGATCAGTATCA
AGGAGCAGATGCTGTGGGACTAGAAGAAAAAACCGAGCAGCACTTAGAAAACAGCCCTGGAAGCAATGAGGACACAGATA
TTCCAAAAGGCTATATGGATTTTATGCTTTTTTATTAACAAATCTGGCTGTGAATGTCTTAATGAAAGTGAGGAGCATGG
ATTTGACAACTGTTTATGAAAAGACATGACCTTCTTGGAATCTGATTAGGATGGACAGCTGCTTATTACTGTCGTCTTCA
ATCAGCCTGTTAAGCTTTATTCAATGAAATTTCAAGGTCCAGATAATGGTCAGGGTCCGAAATACGTAAAAATTTCTATC
AATTTACCCCTATCTATGGATTTTGAAGAGGCAGAAAGAAGTGAACCAATTCCAGCTCTGGAACTATCAGAGGATGATAT
TAAAGAAGATGGTATTGTCCCACTTCATATGTTAAGTTTCAGAATGTTAACAGCATAACTATATTTATTTAGTCCAATCA
AGTGAAGAAGAAACAACTAGAATTTCATATTTTACTTTTATTGGAACTCCAGTCCAGGCAGCAAACATGAATGATTTCAA
ATGAGTAGTTTGCAAAAAAGGAGAAAGCCAC

Alignment

ORF - retro_ttru_1154 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 83.7 %
• Parental protein coverage: 77.51 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  GTAATNNISATPTFLFFRNKVRIDQYQGADAVGLEEKIKQHLENDPGSNEDTDIPKGYMDLMPF-INKAG
          G.AATNN.SA.PT.....NKV..DQYQGADAVGLEEK..QHLEN.PGSNEDTDIPKGYMD.M.F.INK.G
Retrocopy GIAATNNMSAIPTXXXXXNKVTVDQYQGADAVGLEEKTEQHLENSPGSNEDTDIPKGYMDFMLF>INKSG

Parental  CECLNESDEHGFDNCLRKDMTFLESDCDEQLLITVAFNQPVKLYSMKFQGPDNGQGPKYVKIFINLPRSM
          CECLNES.EHGFDNCL.KDMTFLESD.D.QLLITV.FNQPVKLYSMKFQGPDNGQGPKYVKI.INLP.SM
Retrocopy CECLNESEEHGFDNCL*KDMTFLESD*DGQLLITVVFNQPVKLYSMKFQGPDNGQGPKYVKISINLPLSM

Parental  DFEEAERSEPTQALELTEDDIKEDGIVPLR-YVKFQNVNSVTIFVQSNQ-GEEETTRISYFTFIGTPVQA
          DFEEAERSEP..ALEL.EDDIKEDGIVPL..YVKFQNVNS.TIF..SNQ..EEETTRISYFTFIGTPVQA
Retrocopy DFEEAERSEPIPALELSEDDIKEDGIVPLH<YVKFQNVNSITIFI*SNQ<SEEETTRISYFTFIGTPVQA

Parental  TNMNDFKRVVGKKGESH
          .NMNDFK.VV.KKGESH
Retrocopy ANMNDFK*VVCKKGESH

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_1154 retrocopy.

TSS

Tursiops truncatus was not studied using FANTOM5 data.

Lab

retro_ttru_1154 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 6 parental genes, and 8 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000000137	1 retrocopy	retro_cfam_875,
Choloepus hoffmanni	ENSCHOG00000010262	1 retrocopy	retro_chof_1723,
Ictidomys tridecemlineatus	ENSSTOG00000000075	2 retrocopies	retro_itri_302, retro_itri_414,
Tupaia belangeri	ENSTBEG00000017328	2 retrocopies	retro_tbel_1981, retro_tbel_911,
Tursiops truncatus	ENSTTRG00000000119	1 retrocopy	retro_ttru_1378,
Tursiops truncatus	ENSTTRG00000001161	1 retrocopy	retro_ttru_1154 ,