RetrogeneDB ID: retro_tbel_2698

Retrocopy location

• Organism: Treeshrew (Tupaia belangeri)
• Coordinates: scaffold_116908:3642..4468(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: HNRNPD
• Ensembl ID: ENSTBEG00000002327
• Aliases: None
• Description: heterogeneous nuclear ribonucleoprotein D (AU-rich element RNA binding protein 1, 37kDa) [Source:HGNC Symbol;Acc:5036]

Sequence

>retro_tbel_2698
CATTCAGATTCCTCCCCACGACACACTGAAGCAGCGACGGCACAGCAGGAAGAATGGAAAATGTTTATAGGAGGCCTTAG
CTGGGACACTACAAAGAAAGATCTGAAGGACTACTTTTCCAAATTTGGTGAAGTTGTAGACTGCACTCTGAAGTTAGATC
CTATCACAAGGTGATCAAGGGGTTTTGGCTTTGTGCTATTTAAAGAGTTGGAGAGTGTAGATAAGGTCATGGATCAGAAA
GAACCTAAATTGAATAGGAAGGTGATTGATCCTAAAAGGGCCAAAGCCATGAAAACAAAAGAGCCGGTTAAAAAAAATTT
TGTTGGTAGCCTTTCTCCAGACACACCTGAAGAGAAAATAAAGGAGTACTTTGGTGGTTTTGGTGAGGTGGAATCCATAG
AGCTCCCCATGAACAACAAGATCAATCACAGGCATGGGTTCTGCTTTATTACTTTTAAGGAAGACGAACCAGTGAAGAAG
ATAATGAAAAAGAAATACCACAATGTTGGTCTTAGTGAATGTGAAATAAAAGTAGCCATGTCAAAGGAATAGTATCAGCA
ATAGCACCAGTGGGGATCTAGAGGAGGATTTGCAGGAAGAGCTCGTGGAAGAGGTGGTGGCCCCAGTCAAAACTGGAACC
AGGGATATAGTAACTATTGGAATCAAGGCTATGGCAACTATGGATATAACAGCCAAGGTTACGGTGGTTATGGAGGATAT
GACTACACTGGTTACAACAATTACATATGGTGATTATAGCAACCAGCAGAGTGGTTATGGGAAAGTATCCAGGTGAGGTG
GTGATCAAAATAGCTACAAATCATAC

Alignment

ORF - retro_tbel_2698 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 80.58 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 4
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  HSNSSPRHTEAATAQREEWKMFIGGLSWDTTKKDLKDYFSKFGEVVDCTLKLDPITGRSRGFGFVLFKES
          HS.SSPRHTEAATAQ.EEWKMFIGGLSWDTTKKDLKDYFSKFGEVVDCTLKLDPIT..SRGFGFVLFKE.
Retrocopy HSDSSPRHTEAATAQQEEWKMFIGGLSWDTTKKDLKDYFSKFGEVVDCTLKLDPITR*SRGFGFVLFKEL

Parental  ESVDKVMDQKEPKLNGKVIDPKRAQAMKTKEPVKKIFVGGFSPDPPQEKIRQYFAGSGAVESIEL-MDNK
          ESVDKVMDQKEPKLN.KVIDPKRA.AMKTKEPV...FVG..SPD.P.EKI..YF.G.G.VESIEL.M.NK
Retrocopy ESVDKVMDQKEPKLNRKVIDPKRAKAMKTKEPVXXXFVGSLSPDTPEEKIKEYFGGFGEVESIELPMNNK

Parental  TNKRRGFCF-TFKEEEPVKKIMEKKYH-VGLSRCEIKVAMSKEQYQQQQQWGSRGGFAGRARGRGGGPSQ
          .N.R.GFCF.TFKE.EPVKKIM.KKYH.VGLS.CEIKVAMSKE.YQQ..QWGSRGGFAGRARGRGGGPSQ
Retrocopy INHRHGFCFITFKEDEPVKKIMKKKYHNVGLSECEIKVAMSKE*YQQ*HQWGSRGGFAGRARGRGGGPSQ

Parental  NWNQGYSNYWNQGYGNYGYNSQGYGGYGGYDYTGYNNY-YGYGDYSNQQSGYGKVSRRGGHQNSYKPY
          N................GYNSQGYGGYGGYDYTGYNNY.YG..DYSNQQSGYGKVSR.GG.QNSYK.Y
Retrocopy NXXXXXXXXXXXXXXXXGYNSQGYGGYGGYDYTGYNNY>YG--DYSNQQSGYGKVSR*GGDQNSYKSY

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_2698 retrocopy.

TSS

Tupaia belangeri was not studied using FANTOM5 data.

Lab

retro_tbel_2698 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 5 parental genes, and 40 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000015165	1 retrocopy	retro_cjac_2796,
Sarcophilus harrisii	ENSSHAG00000013312	1 retrocopy	retro_shar_752,
Tupaia belangeri	ENSTBEG00000002327	1 retrocopy	retro_tbel_2698 ,
Tupaia belangeri	ENSTBEG00000002817	7 retrocopies	retro_tbel_2079, retro_tbel_2283, retro_tbel_2608, retro_tbel_2874, retro_tbel_3344, retro_tbel_4302, retro_tbel_4405,
Tupaia belangeri	ENSTBEG00000008238	30 retrocopies	retro_tbel_1219, retro_tbel_156, retro_tbel_162, retro_tbel_1643, retro_tbel_1830, retro_tbel_1967, retro_tbel_2192, retro_tbel_2195, retro_tbel_2211, retro_tbel_2330, retro_tbel_261, retro_tbel_2666, retro_tbel_2673, retro_tbel_2703, retro_tbel_276, retro_tbel_2774, retro_tbel_2787, retro_tbel_2970, retro_tbel_3473, retro_tbel_3976, retro_tbel_3995, retro_tbel_4266, retro_tbel_4271, retro_tbel_453, retro_tbel_4653, retro_tbel_4729, retro_tbel_692, retro_tbel_70, retro_tbel_79, retro_tbel_839,