RetrogeneDB ID: retro_tbel_2488

Retrocopy location

• Organism: Treeshrew (Tupaia belangeri)
• Coordinates: scaffold_111810:7387..8431(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: SGCE
• Ensembl ID: ENSTBEG00000008912
• Aliases: None
• Description: sarcoglycan, epsilon [Source:HGNC Symbol;Acc:10808]

Sequence

>retro_tbel_2488
ATGCAGTTCCCCGGGTGGTGGGAGCTGGGAGACTCCTGTACTTGGACCAGACAGGGTCAGGGGACACGCAGGATGAGCCC
TGTGACCACTGGCACATTCTTGCTGGCAGTGTATACCATTTTTTCGAAGGTGCACTCTGATCGGAATGTATACCCATCTG
CAGGTGTCCTCTTTGTCCATGTTTTGGAAAGAGAGCACTTTAAGGGGGAATTTCCACCTTACCCCAAACCTGGTGAGATT
AGTAATGATCCCATAATGAGCCCATTTAATACTAATTTAATGGGCTACCCAGATCGACCTGGATGGCTTCGATATATCCA
AAGGACTCCATATAGTGATGGAGTCTTATATGGGTCTCCAACAGCTGAAAATGTGGGAAAACCAACTATCATTGAGATAA
CTGCTGATAACAGGCGTACCTTTGAGACTGCAAGGCATAATTTGATAATTAATATAATGTCAGCAGAAGATTTCCCATTG
CCATATCATGCTGATTCTTCATTAAAAATATGAATGTAGAAGAAATGTTGGCCAGAGAGGTTCTTGGAAGACTTTCTTGG
GACAGTGAAAAATGTGTGGTAGCCAGAGTGTCTGAATGCCATAAACGTCACGTCGGCCTTCAACACGAGTGGCAGGGTTC
CACTCCCTATTAATGACGTGAAGGAGGGAGTTTATGTCATGGTTGGTGCTGACGTCCCATTTTCTTCTTGTTTACGAGAA
GTTGAAAATCCACAGAATCAGCTAAGATGCAGTCAAGAAATGGAGCCTGTAATAACATGTGATAAGAAGTTTCATACCCA
GTTTTACATTGACTGGTGCAAAATTTCATTGGTTGATAAAACAAAGCAAGTGTCTACCTATCAGGAAGTGATTCATGGAG
AGGGGATTTTACCCGATGGTGGAGAGTACAAACCTCCTTCTGATTCCTTGAAAAGCAGAGACTATTACACGGATTTTCTA
ATTACACTGGCTGTGCCCTTGGCAGTAGCACTGGTCCTTTTTCTAATACTTGCATATATTATGTGCTGCCGACGGGAAGG
TGTG

Alignment

ORF - retro_tbel_2488 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 87.43 %
• Parental protein coverage: 82.77 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  MQFPRWWELGDPCAWTGQGQGTRRMSPATTGTFLLTVYTIFSKVHSDRNVYPSAGVLFVHVLEREHFKGE
          MQFP.WWELGD.C.WT.QGQGTRRMSP.TTGTFLL.VYTIFSKVHSDRNVYPSAGVLFVHVLEREHFKGE
Retrocopy MQFPGWWELGDSCTWTRQGQGTRRMSPVTTGTFLLAVYTIFSKVHSDRNVYPSAGVLFVHVLEREHFKGE

Parental  FPPYPKPGEISNDPIT--FNTNLMGYPDRPGWLRYIQRTPYSDGVLYGSSTAENVGKPTIIEITAYNRRT
          FPPYPKPGEISNDPI...FNTNLMGYPDRPGWLRYIQRTPYSDGVLYGS.TAENVGKPTIIEITA.NRRT
Retrocopy FPPYPKPGEISNDPIMSPFNTNLMGYPDRPGWLRYIQRTPYSDGVLYGSPTAENVGKPTIIEITADNRRT

Parental  FETARHNLIINIMSAEDFPLPYQAE-FFIKNMNVEEMLASEVLG-DFLGAVKNVWQPERLNAINITSALD
          FETARHNLIINIMSAEDFPLPY.A..FFIKNMNVEEMLA.EVLG.DFLG.VKNVW.PE.LNAIN.TSA..
Retrocopy FETARHNLIINIMSAEDFPLPYHAD<FFIKNMNVEEMLAREVLG>DFLGTVKNVW*PECLNAINVTSAFN

Parental  RGGRVPLPINDMKEGVYVMVGADVPFSSCLREVENPQNQLRCSQEMEPVITCDKKFRTQFYIDWCKISLX
          ..GRVPLPIND.KEGVYVMVGADVPFSSCLREVENPQNQLRCSQEMEPVITCDKKF.TQFYIDWCKISL.
Retrocopy TSGRVPLPINDVKEGVYVMVGADVPFSSCLREVENPQNQLRCSQEMEPVITCDKKFHTQFYIDWCKISLV

Parental  XXTKQGSTYQEV-RGEVILPDVEEYQPPDS--KSRDYYTDF-ITLAVPSAVALVHFLILAY-MCCRREGV
          ..TKQ.STYQEV..GE.ILPD..EY.PP....KSRDYYTDF.ITLAVP.AVALV.FLILAY.MCCRREGV
Retrocopy DKTKQVSTYQEVIHGEGILPDGGEYKPPSDSLKSRDYYTDFLITLAVPLAVALVLFLILAYIMCCRREGV

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_2488 retrocopy.

TSS

Tupaia belangeri was not studied using FANTOM5 data.

Lab

retro_tbel_2488 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 2 parental genes, and 2 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000013426	1 retrocopy	retro_cjac_2735,
Tupaia belangeri	ENSTBEG00000008912	1 retrocopy	retro_tbel_2488 ,