RetrogeneDB ID: retro_tbel_3799

Retrocopy location

• Organism: Treeshrew (Tupaia belangeri)
• Coordinates: scaffold_15925:126520..127174(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: GOT2
• Ensembl ID: ENSTBEG00000001808
• Aliases: None
• Description: glutamic-oxaloacetic transaminase 2, mitochondrial [Source:HGNC Symbol;Acc:4433]

Sequence

>retro_tbel_3799
TCTACCAGAGCCAACTCCTGGTGGGCCCATGTGGAAATGGGACCCCTAGATCCCATCCTGGGAGTCACCGAAGCCTTTAA
AAGGGACACCAACAGCAACAAAATGAATCTGGGAGTTGGTGCCTACCGGGAGGACAACGGAAAGCCTTATGTGCTCCCTA
GTGTCCGGAAAGCAGAAGCTCAGATTGCTGCAAAAAGTTTTGACAAGGAATACCTGCCCATTGGAGGACTGGCTGAATTC
TGCAAGGCATCTGCAGAACTGGCGCTGGGTGAGAACAGCGAAGTGTTTAAAAGTGGCTGGTTTGTCACTGTACAGACCAT
TTCTGGAACTGGAGCCTTAAGGATCGGAGCCAGTTTTCTGCAAAGATTTTTTAAGTTCAGCCGAGATGTCTTCCTGCCCA
AACCATCCTGGGGCAATCACACACCCATCTTCAGGGATGCTGGCATGCAGCTACAAGGTTATCGATACTACCCTAAGACT
TGTGGTTTTGACTTCTCAGGCGCTATGGATGACATTTCAAAAATTCCAGAGAAAAGTGTTATTCTCCTGCATGCCTGTGC
CCATAATCCCACAGGAGTCGACCCTCTCCAAGAGCAGTGGAAGGAGATCGCAACAGTGGTGAAGAAAAAGAATCTCTTTG
CTTTCTTTGACATG

Alignment

ORF - retro_tbel_3799 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 90.87 %
• Parental protein coverage: 53.37 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  SNRANSWWAHVEMGPPDPILGVTEAFKRDTNSKKMNLGVGAYRDDNGKPYVLPSVRKAEAQIAAKNFDKE
          S.RANSWWAHVEMGP.DPILGVTEAFKRDTNS.KMNLGVGAYR.DNGKPYVLPSVRKAEAQIAAK.FDKE
Retrocopy STRANSWWAHVEMGPLDPILGVTEAFKRDTNSNKMNLGVGAYREDNGKPYVLPSVRKAEAQIAAKSFDKE

Parental  YLPIGGLS-FCKASADLALCV-SELFKSR-FVTVQTISGTGALRIGASFLQ--FKFSRDVFLPKPSWGNH
          YLPIGGL..FCKASA.LAL...SE.FKS..FVTVQTISGTGALRIGASFLQ..FKFSRDVFLPKPSWGNH
Retrocopy YLPIGGLAEFCKASAELALGENSEVFKSGWFVTVQTISGTGALRIGASFLQRFFKFSRDVFLPKPSWGNH

Parental  TPIFRDAGMQLQGYRYYDPKTCGFDFSGAMDDISKIPEKSVLLLHACAHNPTGVDPRQEQWKEIAAVVKK
          TPIFRDAGMQLQGYRYY.PKTCGFDFSGAMDDISKIPEKSV.LLHACAHNPTGVDP.QEQWKEIA.VVKK
Retrocopy TPIFRDAGMQLQGYRYY-PKTCGFDFSGAMDDISKIPEKSVILLHACAHNPTGVDPLQEQWKEIATVVKK

Parental  KNLFAFFDM
          KNLFAFFDM
Retrocopy KNLFAFFDM

Legend:

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

Expression

RNA-Seq

Tupaia belangeri was not studied using RNA-Seq expression data.

ChIP-Seq

Tupaia belangeri was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_tbel_3799 retrocopy.

TSS

Tupaia belangeri was not studied using FANTOM5 data.

Lab

retro_tbel_3799 was not experimentally validated.

Homology

Retrocopy orthology:

Tupaia belangeri 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 11 parental genes, and 19 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000017346	3 retrocopies	retro_amel_1805, retro_amel_815, retro_amel_846,
Canis familiaris	ENSCAFG00000008357	2 retrocopies	retro_cfam_586, retro_cfam_816,
Callithrix jacchus	ENSCJAG00000011234	1 retrocopy	retro_cjac_2916,
Gorilla gorilla	ENSGGOG00000005767	3 retrocopies	retro_ggor_2912, retro_ggor_449, retro_ggor_774,
Macaca mulatta	ENSMMUG00000006000	1 retrocopy	retro_mmul_1337,
Mustela putorius furo	ENSMPUG00000004862	1 retrocopy	retro_mputfur_567,
Oryctolagus cuniculus	ENSOCUG00000003871	1 retrocopy	retro_ocun_1516,
Otolemur garnettii	ENSOGAG00000000551	2 retrocopies	retro_ogar_2182, retro_ogar_827,
Pongo abelii	ENSPPYG00000007413	3 retrocopies	retro_pabe_3640, retro_pabe_823, retro_pabe_901,
Rattus norvegicus	ENSRNOG00000011782	1 retrocopy	retro_rnor_2695,
Tupaia belangeri	ENSTBEG00000001808	1 retrocopy	retro_tbel_3799 ,