RetrogeneDB ID: retro_ttru_1563

Retrocopy location

• Organism: Dolphin (Tursiops truncatus)
• Coordinates: scaffold_116386:164728..165076(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: GABARAPL1
• Ensembl ID: ENSTTRG00000009099
• Aliases: None
• Description: GABA(A) receptor-associated protein like 1 [Source:HGNC Symbol;Acc:4068]

Sequence

>retro_ttru_1563
ATGAAGTTCGTGTATAAAGAGGAGCATCCTTTCGAGAAGCGGCGCTCTGAGGGCGAGAAGATCCGAAAGAAATACCCGGA
CCGGTTCCCGGTGATCGTTGAAAAGGCTCCCAGATCTCGGATAGGAGACCTGGACAAAAGGAAATGCCTGCTGCCTTCTG
ATCTTACAGTTGGTCAGTTCTACTTCTTGATCCAGAAGCGAATTCATCTCCGAGCTGAGGATGACTTGTTTTTCTTTGTC
AACAATGTCATTCCACCCACGAGTGCCGGGATGGGTCAGCTATACCAGGAACACCATGAAGAAGACTTCTTTCTATATGT
TGCCTCCAGTGATGAAAGTGTCTACGGT

Alignment

ORF - retro_ttru_1563 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 81.03 %
• Parental protein coverage: 99.15 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MKFQYKEDHPFEYRKKEGEKIRKKYPDRVPVIVEKAPKARVPDLDKRKYLVPSDLTVGQFYFLIRKRIHL
          MKF.YKE.HPFE.R..EGEKIRKKYPDR.PVIVEKAP..R..DLDKRK.L.PSDLTVGQFYFLI.KRIHL
Retrocopy MKFVYKEEHPFEKRRSEGEKIRKKYPDRFPVIVEKAPRSRIGDLDKRKCLLPSDLTVGQFYFLIQKRIHL

Parental  RPEDALFFFVNNTIPPTSATMGQLYEDNHEEDYFLYVAYSDESVYG
          R.ED.LFFFVNN.IPPTSA.MGQLY...HEED.FLYVA.SDESVYG
Retrocopy RAEDDLFFFVNNVIPPTSAGMGQLYQEHHEEDFFLYVASSDESVYG

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_1563 retrocopy.

TSS

Tursiops truncatus was not studied using FANTOM5 data.

Lab

retro_ttru_1563 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 11 retrocopies.

Species	Parental gene accession	Retrocopies number
Macaca mulatta	ENSMMUG00000002197	1 retrocopy	retro_mmul_2235,
Oryctolagus cuniculus	ENSOCUG00000016834	3 retrocopies	retro_ocun_1380, retro_ocun_496, retro_ocun_697,
Sarcophilus harrisii	ENSSHAG00000007434	1 retrocopy	retro_shar_82,
Ictidomys tridecemlineatus	ENSSTOG00000002246	1 retrocopy	retro_itri_391,
Tursiops truncatus	ENSTTRG00000008821	2 retrocopies	retro_ttru_1336, retro_ttru_1454,
Tursiops truncatus	ENSTTRG00000009099	3 retrocopies	retro_ttru_1451, retro_ttru_1563 , retro_ttru_1629,