RetrogeneDB ID: retro_tbel_3512

Retrocopy location

• Organism: Treeshrew (Tupaia belangeri)
• Coordinates: scaffold_14319:3381..4274(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: NIF3L1
• Ensembl ID: ENSTBEG00000000704
• Aliases: None
• Description: NIF3 NGG1 interacting factor 3-like 1 (S. cerevisiae) [Source:HGNC Symbol;Acc:13390]

Sequence

>retro_tbel_3512
AGTTGGAACAATGTTTTACTGGCAGAATCAAGCTCCCCTTACAGGGTAAATGCCCTTTCCCTGACCAGCGACTTGACAGT
GAAAGTGATGGAAGAGGCACTGCAAAAGAAAGCAGATCTCAATCTCTTACTGCCTGCCTATTTTCTGACCCATAAAAAGA
ATAAACTGGAAAACCTGGGAGGAGCACTGGATGATTTAGCCTCTGGAGAACAGAGTCAGTGTCAACTGTCCTTATAGACC
CTATGCTGCTATGCCACTGGGAATCAACAACTGTTGGCTGAAGGGCTTGGAGTTTCCACCTCCAGGTCCATACAACTTTC
CAAAGCTCCTAGCTATCCCACAGATAGGACCCACAAAGCAGAATTCAGTGTTAACCATGCCCAAGGCCTGGACAAAGTCA
TATATACAGAGAAAGGAATTACAGATGTTTCCCTTAGGATTTTTTTCTGCTAGGATTGATGATGAGTAACAAATTAAGAC
TAGACTGAATTGTATTTAGAAGGCTTTGATGCAGGTGATGGTTTTTCTTTTCCAGAACAGATAATTTTATCAGAAGACAA
AATTCTGTCACTGGAGAAGCCAGTGCTGCCACACGATGGAATGGGACGGTTATGGACAGTCAGAAAATTTGCCTCCTTGG
CAACCATGATTGAGCAAATTGAAAAACATCTGAAATGATCTTTTGTTCGCTTAGTTCTTGGAGTCAGGAGGACTGCACAG
TCCCAAGTCACAGACATTACCCTGTGTGCTAGCTCTGGGAGAAGCATTCTGCAGGTTGTAGAGACCGACCTCTACGTCAC
AGGTCAGAGATCCCATCATGACATTTGGGATGCTTTTTTCAGGGAATAAACATCATTCTTTGTGAACATAGCAACACCAA
ATGAGGTTTTCTT

Alignment

ORF - retro_tbel_3512 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 60.98 %
• Parental protein coverage: 79.58 %
• Number of stop codons detected: 6
• Number of frameshifts detected: 5

Retrocopy - Parental Gene Alignment:

Parental  SWDNVGLLVEPSPPHMVNTLFLTNDLTEEVMEEALQKKADLILSYHPPIFRPMK-RITWKTWKERLVIRA
          SW.NV.LL.E.S.P..VN.L.LT.DLT..VMEEALQKKADL.L...P..F...K.RI.WKTW.E...I..
Retrocopy SWNNV-LLAESSSPYRVNALSLTSDLTVKVMEEALQKKADLNLLL-PAYFLTHK>RINWKTWEEHWMI*P

Parental  LENRVGIYSPHTAYDAAPQGVNT-WLAKGLGVCTSRPIHPSKALSYPTEGTHRVEFSINHAQDLDKVISA
          LENRV....P...Y.A.P.G.N...LA.GLGV.TSR.I..SKA.SYPT..TH..EFS.NHAQ.LDKVI..
Retrocopy LENRVSVNCPYRPYAAMPLGINN<LLAEGLGVSTSRSIQLSKAPSYPTDRTHKAEFSVNHAQGLDKVIYT

Parental  VKGIVDVSVT-SFPARIDDEEQTRISLNCTQKALMQVVAFLSQNRQLYQKT-EILSLEKPLLLHTGMGRL
          .KGI.DVS....F.ARIDDE.Q....LNC..KALMQV..FL.QNR..YQKT..ILSLEKP.L.H.GMGRL
Retrocopy EKGITDVSLR>FFSARIDDE*QIKTRLNCI*KALMQVMVFLFQNR*FYQKT<KILSLEKPVLPHDGMGRL

Parental  CTLEESVSLATMIERIKRHLKLSHVRLALGAGRTLESQVRVVAVCAGSGSSVLQGVEADLYLTGEMSHHD
          .T.....SLATMIE.I..HLK.S.VRL.LG..RT..SQV.....CA.SG.S.LQ.VE.DLY.TG..SHHD
Retrocopy WTVRKFASLATMIEQIEKHLK*SFVRLVLGVRRTAQSQVTDITLCASSGRSILQVVETDLYVTGQRSHHD

Parental  VLDA-ASQGINVILCEHSNSERGFL
          ..DA...QGIN.ILCEHSN...GFL
Retrocopy IWDA<FFQGINIILCEHSNTK*GFL

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_3512 retrocopy.

TSS

Tupaia belangeri was not studied using FANTOM5 data.

Lab

retro_tbel_3512 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 6 parental genes, and 21 retrocopies.

Species	Parental gene accession	Retrocopies number
Felis catus	ENSFCAG00000023186	1 retrocopy	retro_fcat_589,
Macaca mulatta	ENSMMUG00000006639	1 retrocopy	retro_mmul_444,
Nomascus leucogenys	ENSNLEG00000006935	1 retrocopy	retro_nleu_1504,
Oryctolagus cuniculus	ENSOCUG00000010667	16 retrocopies	retro_ocun_1105, retro_ocun_1534, retro_ocun_1539, retro_ocun_1691, retro_ocun_1692, retro_ocun_1710, retro_ocun_1729, retro_ocun_1749, retro_ocun_1789, retro_ocun_1828, retro_ocun_1837, retro_ocun_1841, retro_ocun_1846, retro_ocun_1847, retro_ocun_1854, retro_ocun_929,
Pongo abelii	ENSPPYG00000013063	1 retrocopy	retro_pabe_244,
Tupaia belangeri	ENSTBEG00000000704	1 retrocopy	retro_tbel_3512 ,