RetrogeneDB ID: retro_tsyr_234

Retrocopy location

• Organism: Tarsier (Tarsius syrichta)
• Coordinates: GeneScaffold_5965:8676..9021(-)
• Located in intron of: ENSTSYG00000011098

Retrocopy information

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

Parental gene information

• Parental gene symbol: GABARAPL1
• Ensembl ID: ENSTSYG00000005307
• Aliases: None
• Description: GABA(A) receptor-associated protein like 1 [Source:HGNC Symbol;Acc:4068]

Sequence

>retro_tsyr_234
ATGAAGTTCCAGTATCAGGAGGACCATCCCTTCGAATATCGGAAAAAGGAAGGAGAAAAGATCCGGAAGGAATATCCGGA
CAGGGTCCCTGTGATCGTGGAGAAGGCTCCGAGAGCCAGGGTGCCTGATCTGGACAAGCGGAAGTACCTAGTGCCCTCTG
ACCTCCCTGTTGGCCAGTTCGACTTCTTAATCCGGAAGAGGAGCCACCTGAGACCTGAGGACGCCTTATTTTTCTTTGTC
AACAACACTACCCCTCCCACTAGTGCTGCGATGGGCCAGCTGTATGAGGACAACCATGAGGAAGACTATTTTCTGCATGT
GGCCTACAGTGATGAGAGTCTATGG

Alignment

ORF - retro_tsyr_234 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 90.43 %
• Parental protein coverage: 98.29 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MKFQYKEDHPFEYRKKEGEKIRKKYPDRVPVIVEKAPKARVPDLDKRKYLVPSDLTVGQFYFLIRKRIHL
          MKFQY.EDHPFEYRKKEGEKIRK.YPDRVPVIVEKAP.ARVPDLDKRKYLVPSDL.VGQF.FLIRKR.HL
Retrocopy MKFQYQEDHPFEYRKKEGEKIRKEYPDRVPVIVEKAPRARVPDLDKRKYLVPSDLPVGQFDFLIRKRSHL

Parental  RPEDALFFFVNNTIPPTSATMGQLYEDNHEEDYFLYVAYSDESVY
          RPEDALFFFVNNT.PPTSA.MGQLYEDNHEEDYFL.VAYSDES..
Retrocopy RPEDALFFFVNNTTPPTSAAMGQLYEDNHEEDYFLHVAYSDESLW

Legend:

• *: Stop codon
• >: Forward frameshift by one nucleotide
• <: Reverse frameshift by one nucleotide

Expression

RNA-Seq

Tarsius syrichta was not studied using RNA-Seq expression data.

ChIP-Seq

Tarsius syrichta was not studied using ChIP-Seq data.

EST

Tarsius syrichta was not studied using EST data.

TSS

Tarsius syrichta was not studied using FANTOM5 data.

Lab

retro_tsyr_234 was not experimentally validated.

Homology

Retrocopy orthology:

Tarsius syrichta 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 26 retrocopies.

Species	Parental gene accession	Retrocopies number
Cavia porcellus	ENSCPOG00000006718	1 retrocopy	retro_cpor_232,
Homo sapiens	ENSG00000139112	1 retrocopy	retro_hsap_60,
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,
Tarsius syrichta	ENSTSYG00000005307	19 retrocopies	retro_tsyr_1045, retro_tsyr_1070, retro_tsyr_1101, retro_tsyr_1137, retro_tsyr_1308, retro_tsyr_1413, retro_tsyr_1467, retro_tsyr_1481, retro_tsyr_1671, retro_tsyr_1765, retro_tsyr_1800, retro_tsyr_234 , retro_tsyr_573, retro_tsyr_761, retro_tsyr_796, retro_tsyr_832, retro_tsyr_864, retro_tsyr_978, retro_tsyr_999,