RetrogeneDB ID: retro_tbel_4413

Retrocopy location

• Organism: Treeshrew (Tupaia belangeri)
• Coordinates: scaffold_81582:9494..10228(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSTBEG00000003474
• Aliases: None
• Description: None

Sequence

>retro_tbel_4413
CTGAATATTTCCTTCCCAGCCACGGGCTGCCAGAAACTCATTGAAGTGGACGATGAACGCAAACTTCGTACTTTTTATGA
GAAGCGTATGGCCACAGAAGTTGCTGCTGACGCTTTGGGCGAAGAATGGAAGGGTTATGTAGTCCGAATCAGTGGTGGAA
ACGACAAACAAGGTTTCCCCATGAAGCAGGGCGTCTTGACCCACGGCCGTGTCCGCCTTCTACTGAGTAAGGGACATTCC
TGTTACAGACCAAGGAGAACTGGAGAAAGAAAGCGCAAATCTGTTCGGGGTTGCATTGTGGATGCCAACCTGAGCATTCT
CAACTTGGTTATTGTTAAAAAAGGAGAGAAGGATATTCCAGGACTGACTGATACTACCGTGCCTCGTCGCCTGGGGCCTA
AGAGAGCTAGCAGAATCCGAAAACTTTTCAATCTCTCTAAAGAAGACGATGTCCACCAATATGTTGTAAGAAAGCCCTTA
AATAAAGAAGGTAAGAAACCTAGGACCAAAGCACCCAAGATTCAGCGTCTTGTGACTCCCCGTGTCCTGCAACACAAACG
CCGGCGTATTGCCCTCAAGAAACAACGTACTAAGAAAAATAAGGAAGAGGCAGCAGAATATGCTAAACTTTTGGCCAAGA
GACGAAGGAGGCTAAAGAAAAACGCCAAGAACAGATTCCAAGAGACGCAGGCTGAACCTCTCTGAGAGCTTCCACTTCTA
AGTCTGAATCCAGT

Alignment

ORF - retro_tbel_4413 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 89.92 %
• Parental protein coverage: 99.18 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  LNISFPATGCQKLIEVDDERKLRTFYEKRMATEVAADALGEEWKGYVVRISGGNDKQGFPMKQGVLTHGR
          LNISFPATGCQKLIEVDDERKLRTFYEKRMATEVAADALGEEWKGYVVRISGGNDKQGFPMKQGVLTHGR
Retrocopy LNISFPATGCQKLIEVDDERKLRTFYEKRMATEVAADALGEEWKGYVVRISGGNDKQGFPMKQGVLTHGR

Parental  VRLLLSKGHSCYRPRRTGE-KRKSVRGCTVDANLSILNSVIVKK-EKNIPGLTDTTVPRHLGPKRASRIP
          VRLLLSKGHSCYRPRRTGE.KRKSVRGC.VDANLSILN.VIVKK.EK.IPGLTDTTVPR.LGPKRASRI.
Retrocopy VRLLLSKGHSCYRPRRTGERKRKSVRGCIVDANLSILNLVIVKKGEKDIPGLTDTTVPRRLGPKRASRIR

Parental  KLFNLSKEDDVRQYVVRKPLNKEGKNPRTKAPKIQCLVTPCVLQHKRWHTALKKQRTKKNKEEAADYAQL
          KLFNLSKEDDV.QYVVRKPLNKEGK.PRTKAPKIQ.LVTP.VLQHKR...ALKKQRTKKNKEEAA.YA.L
Retrocopy KLFNLSKEDDVHQYVVRKPLNKEGKKPRTKAPKIQRLVTPRVLQHKRRRIALKKQRTKKNKEEAAEYAKL

Parental  LAKR-MKEAKEKSQEQ-TVKRRRL-SPLRASTSKSESS
          LAKR..KEAKEK.QEQ...KRRRL...LRASTSKSESS
Retrocopy LAKR<TKEAKEKRQEQ<DSKRRRL>TSLRASTSKSESS

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

1 EST(s) were mapped to retro_tbel_4413 retrocopy

EST ID	Start	End	Identity	Match	Mis-match	Score
CF526854	9565	9883	99.1	314	3	310

TSS

Tupaia belangeri was not studied using FANTOM5 data.

Lab

retro_tbel_4413 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 9 parental genes, and 51 retrocopies.

Species	Parental gene accession	Retrocopies number
Anolis carolinensis	ENSACAG00000017634	1 retrocopy	retro_acar_20,
Cavia porcellus	ENSCPOG00000003750	4 retrocopies	retro_cpor_1244, retro_cpor_22, retro_cpor_317, retro_cpor_486,
Dasypus novemcinctus	ENSDNOG00000007241	1 retrocopy	retro_dnov_1192,
Ficedula albicollis	ENSFALG00000003078	1 retrocopy	retro_falb_24,
Loxodonta africana	ENSLAFG00000010766	4 retrocopies	retro_lafr_1021, retro_lafr_1239, retro_lafr_59, retro_lafr_667,
Monodelphis domestica	ENSMODG00000004095	1 retrocopy	retro_mdom_301,
Ochotona princeps	ENSOPRG00000012290	5 retrocopies	retro_opri_123, retro_opri_642, retro_opri_78, retro_opri_862, retro_opri_895,
Sarcophilus harrisii	ENSSHAG00000005486	1 retrocopy	retro_shar_549,
Tupaia belangeri	ENSTBEG00000003474	33 retrocopies	retro_tbel_1380, retro_tbel_1384, retro_tbel_1729, retro_tbel_1747, retro_tbel_1899, retro_tbel_1907, retro_tbel_2051, retro_tbel_2444, retro_tbel_2621, retro_tbel_2753, retro_tbel_2848, retro_tbel_3148, retro_tbel_316, retro_tbel_3165, retro_tbel_3271, retro_tbel_3497, retro_tbel_3591, retro_tbel_3747, retro_tbel_3792, retro_tbel_3866, retro_tbel_3883, retro_tbel_411, retro_tbel_4208, retro_tbel_4242, retro_tbel_4413 , retro_tbel_4467, retro_tbel_4570, retro_tbel_485, retro_tbel_492, retro_tbel_576, retro_tbel_743, retro_tbel_824, retro_tbel_828,