RetrogeneDB ID: retro_tsyr_2003

Retrocopy location

• Organism: Tarsier (Tarsius syrichta)
• Coordinates: scaffold_77561:6802..7182(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: MYL1
• Ensembl ID: ENSTSYG00000007599
• Aliases: None
• Description: myosin, light chain 1, alkali; skeletal, fast [Source:HGNC Symbol;Acc:7582]

Sequence

>retro_tsyr_2003
GAGGGCCAGATCCTGTACAGCCAGTGTGGGGACGTGATGAGGGCCCTGGGCTAGATCCCACCAACGCTGAGGTCCTCAAG
GTCCTGGGGAACTCCAGGGGTGATGAGATGAATGTGAAGGTGCTGGACTTTGAGCACTTCCTGCCCATGCTCCAGACTGT
GGCCAAGAACAAGGACCAGGGCACCTATGAGGATTATGTTGAAGGACTTCAGGCATTTGACAAGGAAGGGAACGGCACAG
TGATGGGTGCGGAAATCCAGCATGTCCTTGTCACTCTGGGCGAGACGATGACAGAGGAAGAAGTAGAGATGCTGGTGGCA
GGGCATGAGGACAGCAATGGTTGTATCAACTATGCAGAGCTGGTCTGTATGGTGCTGAAT

Alignment

ORF - retro_tsyr_2003 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 65.62 %
• Parental protein coverage: 67.91 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  ESKITLSQVGDVLRALG-TNPTNAEVRKVLGNPSNEEMNAKKIEFEQFLPMMQAISNNKDQGTYEDFVEG
          E..I..SQ.GDV.RALG...PTNAEV.KVLGN....EMN.K...FE.FLPM.Q....NKDQGTYED.VEG
Retrocopy EGQILYSQCGDVMRALG<LDPTNAEVLKVLGNSRGDEMNVKVLDFEHFLPMLQTVAKNKDQGTYEDYVEG

Parental  LRVFDKEGNGTVMGAELRHVLATLGEKMKEEEVEALMKGQEDSNGCINYEAFVKHIMS
          L..FDKEGNGTVMGAE..HVL.TLGE.M.EEEVE.L..G.EDSNGCINY...V.....
Retrocopy LQAFDKEGNGTVMGAEIQHVLVTLGETMTEEEVEMLVAGHEDSNGCINYAELVCMVLN

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_2003 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 5 parental genes, and 12 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000008609	2 retrocopies	retro_chof_1485, retro_chof_2467,
Macropus eugenii	ENSMEUG00000006905	5 retrocopies	retro_meug_1796, retro_meug_21, retro_meug_537, retro_meug_87, retro_meug_914,
Mus musculus	ENSMUSG00000061816	1 retrocopy	retro_mmus_973,
Sorex araneus	ENSSARG00000002568	1 retrocopy	retro_sara_196,
Tarsius syrichta	ENSTSYG00000007599	3 retrocopies	retro_tsyr_1284, retro_tsyr_1539, retro_tsyr_2003 ,