RetrogeneDB ID: retro_tbel_2111

Retrocopy location

• Organism: Treeshrew (Tupaia belangeri)
• Coordinates: scaffold_100649:3605..4501(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: SLC38A2
• Ensembl ID: ENSTBEG00000016388
• Aliases: None
• Description: solute carrier family 38, member 2 [Source:HGNC Symbol;Acc:13448]

Sequence

>retro_tbel_2111
CTGCTGGTGTCACAGATGCCCAGAAATTTAGTATAATTGGGATATACCGGTGGCCTTTCGTTAGTGTGTATGATGTTCTT
TCTGACTGCGCTAATTTGCAAGAAATTTCAGATTCCTTGTCCTCTGGAAGTTGCTTTGACGATCAATGAAACAAGGAATG
GCACTTTAACACAGCCAGCACTGTCTGCATCTGGTCTGTCTTTTAACATGACTGTTGATGATTCTTGCAAACCGTGCTAT
TTTATCTTCAACTCCCAGAACGTCTATGCTGTACTGATCCTGACCTTTTCCTTTGTCTGTCATCCGGCTACTATCCCATC
TATGAAGAGCTGAAAGGCTGCAGCTGTAGAAGAATGATGAATGTGTCCAAGATGTCATGTTTTTGCTGTTTCTCATGCAT
CTGCTTGCCGTCTTCTTTGGATACTTAACATTTTCCAAACACGTTGAGTCAGAATTGCTTCATACCTGCTCTACTGTCCT
GGGAGCCGATGTTCTTCTCATCGTCCGTTTGGCTATGTTAGTGGCTGTCATCCAGATAGTACCAGTTGCTATTTTCCCCA
ACCGGCGTTCCATAACTCATTTGTCTGTTCATTAAAAGATTTCAGTTGGTGGCATCATAGTCTCATTATGGTATCTATCT
TGGCATTTACCGATTTGCTTGTCATCTTCATTCCAACTATTGGGGAGATCTTTGGCTTCGTTGGTGCATCTGCTGCTGCT
ATGTTGATTTTTATTCTTCCATCTGCCTTCTCTGTCAAGTTAGTGAAGAAAGAAACTATGTAATCTATACAAAAGATCGG
GGCAACGTTCTTCCTGTTAGGAGGCATAGTGGTGGTGACGAGAAGCATGGCTTTGATTGTTTGGATTGGGTACACAATGC
TCCTGGAGGTGGTCAT

Alignment

ORF - retro_tbel_2111 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 72.79 %
• Parental protein coverage: 59.33 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  ILPLSLLRNLGYLGYTSGLSLLCMMFFLIVVICKKFQIPCPMEVAFLINETMNGTLTQPTAFASDSTFNM
          .L.....RNL..LGYT.GLSL.CMMFFL...ICKKFQIPCP.EVA..INET.NGTLTQP...AS...FNM
Retrocopy LLVSQMPRNLV*LGYTGGLSLVCMMFFLTALICKKFQIPCPLEVALTINETRNGTLTQPALSASGLSFNM

Parental  TGDDSCRPRYFIFNSQTVYAVPIPDLSFVC-PANPP-IYEELKR-SRKRMMNVSKIS-FFAMFLMYLLAA
          T.DDSC.P.YFIFNSQ.VYAV.I...SFVC.PA..P.IYEELK..S..RMMNVSK.S..F..FLM.LLA.
Retrocopy TVDDSCKPCYFIFNSQNVYAVLILTFSFVCHPATIP<IYEELKGCSCRRMMNVSKMS<MFLLFLMHLLAV

Parental  LFGYLTFYKNVESELLHTYSTVLGTDILLLIVRLAVLMAVVLTVPVVIFPIRSSVTHL-LCSSKDFSWWR
          .FGYLTF.K.VESELLHT.STVLG.D.LL.IVRLA.L.AV...VPV.IFP.R.S.THL..CS.KDFSWW.
Retrocopy FFGYLTFSKHVESELLHTCSTVLGADVLL-IVRLAMLVAVIQIVPVAIFPNRRSITHL<VCSLKDFSWWH

Parental  HSLITVSILAFTNLLVIFVPTIRDIFGFIGASAAAMLIFILPSAFYIKLVKKEPMKSIQKIGAMFFLFCG
          HSLI.VSILAFT.LLVIF.PTI..IFGF.GASAAAMLIFILPSAF..KLVKKE.M.SIQKIGA.FFL..G
Retrocopy HSLIMVSILAFTDLLVIFIPTIGEIFGFVGASAAAMLIFILPSAFSVKLVKKETM*SIQKIGATFFLLGG

Parental  VVVMTGSMALIV-LDWVHNAPGGGH
          .VV.T.SMALIV.LDWVHNAPGGGH
Retrocopy IVVVTRSMALIV<LDWVHNAPGGGH

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_2111 retrocopy.

TSS

Tupaia belangeri was not studied using FANTOM5 data.

Lab

retro_tbel_2111 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 1 parental gene, and 1 retrocopy.

Species	Parental gene accession	Retrocopies number
Tupaia belangeri	ENSTBEG00000016388	1 retrocopy	retro_tbel_2111 ,