RetrogeneDB ID: retro_tsyr_138

Retrocopy location

• Organism: Tarsier (Tarsius syrichta)
• Coordinates: GeneScaffold_3712:36239..36451(+)
• Located in intron of: ENSTSYG00000004760

Retrocopy information

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

Parental gene information

• Parental gene symbol: HMGN2
• Ensembl ID: ENSTSYG00000011519
• Aliases: None
• Description: high mobility group nucleosomal binding domain 2 [Source:HGNC Symbol;Acc:4986]

Sequence

>retro_tsyr_138
AAGGTGAAGGATAAACCACAGAGAAGATCTGCAAGGTTGTCTGCTAAATCTGCTCTTCCAATGACAAAGCCAAGCCTAAA
ACGGCCCCTGAAAAGAAGGGAAAGAAGGTACCCAAAAAGGAAAAGCTGACACCAGCAAGGATAGGATAATCTGCAGAATA
TGGGGACAAAACAGACCAAGCAAAGAAAGTAGAAGGTGCTGGAGATGCCAAG

Alignment

ORF - retro_tsyr_138 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 65.79 %
• Parental protein coverage: 88.24 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  KVKDEPQRRSARLSAKPAPPKPEP-KPKKAPAKKGEKVPKGKKGKADAGKEGNNPAENGDAKTDQAQKAE
          KVKD.PQRRSARLSAK.A.P...P.KPK.AP.KKG.KVP..KK.K......G...AE.GD.KTDQA.K.E
Retrocopy KVKDKPQRRSARLSAKSALPMTKP<KPKTAPEKKGKKVP--KKEKLTPARIG*S-AEYGD-KTDQAKKVE

Parental  GAGDAK
          GAGDAK
Retrocopy GAGDAK

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_138 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 9 parental genes, and 104 retrocopies.

Species	Parental gene accession	Retrocopies number
Dipodomys ordii	ENSDORG00000001787	3 retrocopies	retro_dord_10, retro_dord_401, retro_dord_511,
Felis catus	ENSFCAG00000012812	3 retrocopies	retro_fcat_1842, retro_fcat_4, retro_fcat_530,
Gorilla gorilla	ENSGGOG00000000971	11 retrocopies	retro_ggor_114, retro_ggor_146, retro_ggor_162, retro_ggor_166, retro_ggor_182, retro_ggor_186, retro_ggor_197, retro_ggor_23, retro_ggor_38, retro_ggor_40, retro_ggor_54,
Macropus eugenii	ENSMEUG00000010966	8 retrocopies	retro_meug_1178, retro_meug_126, retro_meug_1859, retro_meug_1910, retro_meug_1997, retro_meug_248, retro_meug_369, retro_meug_76,
Mus musculus	ENSMUSG00000003038	2 retrocopies	retro_mmus_202, retro_mmus_2582,
Otolemur garnettii	ENSOGAG00000032571	14 retrocopies	retro_ogar_1438, retro_ogar_1445, retro_ogar_1603, retro_ogar_1668, retro_ogar_1687, retro_ogar_1998, retro_ogar_2097, retro_ogar_2210, retro_ogar_2231, retro_ogar_2424, retro_ogar_287, retro_ogar_2989, retro_ogar_3411, retro_ogar_52,
Pongo abelii	ENSPPYG00000001682	16 retrocopies	retro_pabe_1182, retro_pabe_1511, retro_pabe_1977, retro_pabe_1989, retro_pabe_206, retro_pabe_2263, retro_pabe_23, retro_pabe_2601, retro_pabe_3, retro_pabe_3480, retro_pabe_366, retro_pabe_396, retro_pabe_533, retro_pabe_535, retro_pabe_589, retro_pabe_696,
Tarsius syrichta	ENSTSYG00000011519	42 retrocopies	retro_tsyr_114, retro_tsyr_1156, retro_tsyr_1165, retro_tsyr_1199, retro_tsyr_1227, retro_tsyr_1255, retro_tsyr_1270, retro_tsyr_13, retro_tsyr_1357, retro_tsyr_138 , retro_tsyr_1382, retro_tsyr_1394, retro_tsyr_143, retro_tsyr_1487, retro_tsyr_1488, retro_tsyr_1506, retro_tsyr_1510, retro_tsyr_1551, retro_tsyr_1618, retro_tsyr_163, retro_tsyr_168, retro_tsyr_1680, retro_tsyr_1878, retro_tsyr_1881, retro_tsyr_1970, retro_tsyr_2019, retro_tsyr_2134, retro_tsyr_256, retro_tsyr_280, retro_tsyr_325, retro_tsyr_333, retro_tsyr_594, retro_tsyr_611, retro_tsyr_668, retro_tsyr_675, retro_tsyr_726, retro_tsyr_772, retro_tsyr_83, retro_tsyr_857, retro_tsyr_927, retro_tsyr_959, retro_tsyr_97,
Tursiops truncatus	ENSTTRG00000005681	5 retrocopies	retro_ttru_1392, retro_ttru_1443, retro_ttru_3, retro_ttru_345, retro_ttru_788,