RetrogeneDB ID: retro_tbel_3550

Retrocopy location

• Organism: Treeshrew (Tupaia belangeri)
• Coordinates: scaffold_144452:44495..45116(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSTBEG00000011048
• Aliases: None
• Description: None

Sequence

>retro_tbel_3550
GATGAGCTGAATGTTCTGGTTCTCAGAGTTGATACCAACCCAATTTGGTGGGTAATGCAAGCATTAGAGGAATCTCAGCT
TACTTTATTCAAATGCATAGATGCTGTCGTCGGTATAGGGCAATTCCCATTTCTCCATGACTCGCTGTGACAAACCTGCT
ATAATAGCAAGTCACACCCAGGAGAGCGGATTCTTGTGTCCTAGAAAGAACATCAGACTTAGAGACGTTTTCAGAGACCC
TGGCAACCCAGTTCCAAATTTAATCCCTCAGGAACTAAAGACAGGAAATATGAGGTGTTGACAGCAGCAAGCAATGCTAT
TGCTGAAGAGTTTAAGGATCTGATGACCAAGAGTGACATAAAGGGTCGCCGTATGGAACTCTGCTGGCTGCATTTCTCCC
CAAAGCCCGTTGTTACATTCATAGGATGAACAAGAAGTTAAAGATAATCAGGAAAAGAAAGCCAGGATCTTGGTGATTGA
GGCTGCAGGAGATAGCACGCTGCAATGCATGACCCTCATGAGTGTCACCTTCACAGTGCAGAAACAGAGTATTTAGATTG
ATGCCTGTGATTTAGATTCTGATTCAGGACTCCTCCAGTAGACTGTGACATCACAGGAGGA

Alignment

ORF - retro_tbel_3550 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 70.42 %
• Parental protein coverage: 68.42 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 5

Retrocopy - Parental Gene Alignment:

Parental  DELNLLVIIVDTNPIWWGKQALKESQFTLSKCIDAVM-VLGNSHLFMNRSNKLAVIASHIQESRFLYPGK
          DELN.LV..VDTNPIWW..QAL.ESQ.TL.KCIDAV..V.GNSH..M.R..K.A.IASH.QES.FL.P.K
Retrocopy DELNVLVLRVDTNPIWWVMQALEESQLTLFKCIDAVV>V*GNSHFSMTRCDKPAIIASHTQESGFLCPRK

Parental  NGRLGDFFGDPGNP-TSEFNPSGSKDGKYELLTAANDIIAEEIKDLMTKSDIKGQHTE-TLLAGSLAKAL
          N.RL.D.F.DPGNP..S.FNPSG.KD.KYE.LTAA...IAEE.KDLMTKSDIKG...E.TLLA..L.KA.
Retrocopy NIRLRDVFRDPGNP<SSKFNPSGTKDRKYEVLTAASNAIAEEFKDLMTKSDIKGRRME<TLLAAFLPKAR

Parental  CYIHRMNK-EVKDNQEMKSRILVIKAAEDSALQYMNFMNVIFAAQKQNILIDACVLDSDSGLLQ-QACDI
          CYIHRMNK.EVKDNQE.K.RILVI.AA.DS.LQ.M..M.V.F..QKQ.I.IDAC.LDSDSGLLQ...CDI
Retrocopy CYIHRMNK<EVKDNQEKKARILVIEAAGDSTLQCMTLMSVTFTVQKQSI*IDACDLDSDSGLLQ<VDCDI

Parental  TGG
          TGG
Retrocopy TGG

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_3550 retrocopy.

TSS

Tupaia belangeri was not studied using FANTOM5 data.

Lab

retro_tbel_3550 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 8 parental genes, and 16 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000006219	2 retrocopies	retro_chof_1726, retro_chof_2064,
Loxodonta africana	ENSLAFG00000007300	1 retrocopy	retro_lafr_292,
Macropus eugenii	ENSMEUG00000013734	1 retrocopy	retro_meug_558,
Myotis lucifugus	ENSMLUG00000004319	1 retrocopy	retro_mluc_183,
Monodelphis domestica	ENSMODG00000023728	1 retrocopy	retro_mdom_1915,
Tupaia belangeri	ENSTBEG00000011048	8 retrocopies	retro_tbel_1645, retro_tbel_1820, retro_tbel_2555, retro_tbel_3550 , retro_tbel_3894, retro_tbel_3931, retro_tbel_4065, retro_tbel_4293,
Tarsius syrichta	ENSTSYG00000007444	1 retrocopy	retro_tsyr_1126,
Tursiops truncatus	ENSTTRG00000007259	1 retrocopy	retro_ttru_1357,