RetrogeneDB ID: retro_tbel_4120

Retrocopy location

• Organism: Treeshrew (Tupaia belangeri)
• Coordinates: scaffold_67885:1481..2313(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: KPNA2
• Ensembl ID: ENSTBEG00000006274
• Aliases: None
• Description: karyopherin alpha 2 (RAG cohort 1, importin alpha 1) [Source:HGNC Symbol;Acc:6395]

Sequence

>retro_tbel_4120
CAGATTCTTCCTACTTTAGTTCGTCTTCTGCATCACGATGATCCCGAAGTATTAGCAGATACCTGCTGGGCCATTTCCTA
CCTTACCAATGGTCCAAATGAATGGATTGAAATAGTTGTGAAAGCAGGAGTTGTGCCCTAACTTGTGAAGCTTCTAGGAG
CTACCGAATTGCCCATTGTGACCCCTGCCCTAAGAGCCATAGGTAATATTGTCACTGGGACAGATGAACAGACCCAGGTT
GTGATAGATGCTGGAGCACTCGCCATCTTCCCCAGCCTTCTGACCAACTCCAAAACAAATATTCAGAAGGAAGCTACGTG
GACCATGTCCAACATCACCGCCGGTCGGCAGGACCAGATCCAGCAGGTTGTGAATCACAGGTTAGTCCTGTTCCTCGTCA
GCGTGCTCTCCAAGGCTGACTTTAAGACGCGGAAGGAGGCTGTGTGGGCTGTGACCAACTACACAAGCGACAGAACAGTG
GAGCAGATTGTATACCTCGTCCACTGTGGCATCATAGAACCGCTGATGAACCTCTTACCTGCGAAAGATACCAAAATTAT
TCTGGTTATTTTGGATGCCATTTCAAATATTTTTCAGGCTGCTGAAAAGCTAGGAGAAACTGAGAAACTTAGTATAATAA
TCGAAGAATATGGAGGCCTGGATAAAAATTGAAGCTCTACAAAACCATGAAAATGAGTCTGTGTACAAGTCTTCATTAAA
CTTGATTGAGAAGTATTTCTCTGTAGAGGAAGAGGAAGATCAGAATGTTGTGCCCAAAACTACCTCTGACAGCTACACCT
TCCAAGTGCGGGATGGGACTCCTGGGGCCTTT

Alignment

ORF - retro_tbel_4120 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 93.17 %
• Parental protein coverage: 52.46 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  EILPTLVRLLHHDDPEVLADTCWAISYLTDGPNERIEMVVKTGVVPQLVKLLGATELPIVTPALRAIGNI
          .ILPTLVRLLHHDDPEVLADTCWAISYLT.GPNE.IE.VVK.GVVP.LVKLLGATELPIVTPALRAIGNI
Retrocopy QILPTLVRLLHHDDPEVLADTCWAISYLTNGPNEWIEIVVKAGVVP*LVKLLGATELPIVTPALRAIGNI

Parental  VTGTDEQTQVVIDAGALAVFPSLLTNSKTNIQKEATWTMSNITAGRQDQIQQVVNHGLVPFLVGVLSKAD
          VTGTDEQTQVVIDAGALA.FPSLLTNSKTNIQKEATWTMSNITAGRQDQIQQVVNH.LV.FLV.VLSKAD
Retrocopy VTGTDEQTQVVIDAGALAIFPSLLTNSKTNIQKEATWTMSNITAGRQDQIQQVVNHRLVLFLVSVLSKAD

Parental  FKTQKEAVWAVTNYTSGGTVEQIVYLVHCGIIEPLMNLLTAKDTKIILVILDAISNIFQAAEKLGETEKL
          FKT.KEAVWAVTNYTS..TVEQIVYLVHCGIIEPLMNLL.AKDTKIILVILDAISNIFQAAEKLGETEKL
Retrocopy FKTRKEAVWAVTNYTSDRTVEQIVYLVHCGIIEPLMNLLPAKDTKIILVILDAISNIFQAAEKLGETEKL

Parental  SIMIEECGGLD-KIEALQNHENESVYKSSLNLIEKYFSVEEEEDQNVVPETTSDSYTFQVQDGTPGAF
          SI.IEE.GGLD.KIEALQNHENESVYKSSLNLIEKYFSVEEEEDQNVVP.TTSDSYTFQV.DGTPGAF
Retrocopy SIIIEEYGGLD>KIEALQNHENESVYKSSLNLIEKYFSVEEEEDQNVVPKTTSDSYTFQVRDGTPGAF

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_4120 retrocopy.

TSS

Tupaia belangeri was not studied using FANTOM5 data.

Lab

retro_tbel_4120 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 15 parental genes, and 48 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000018411	3 retrocopies	retro_amel_1161, retro_amel_1318, retro_amel_440,
Canis familiaris	ENSCAFG00000011598	2 retrocopies	retro_cfam_648, retro_cfam_90,
Cavia porcellus	ENSCPOG00000026318	1 retrocopy	retro_cpor_46,
Dasypus novemcinctus	ENSDNOG00000019151	6 retrocopies	retro_dnov_1184, retro_dnov_1811, retro_dnov_2161, retro_dnov_2279, retro_dnov_379, retro_dnov_693,
Echinops telfairi	ENSETEG00000004445	2 retrocopies	retro_etel_346, retro_etel_347,
Felis catus	ENSFCAG00000001936	2 retrocopies	retro_fcat_1176, retro_fcat_921,
Myotis lucifugus	ENSMLUG00000027946	7 retrocopies	retro_mluc_1034, retro_mluc_1258, retro_mluc_1414, retro_mluc_288, retro_mluc_50, retro_mluc_52, retro_mluc_993,
Macaca mulatta	ENSMMUG00000018256	3 retrocopies	retro_mmul_1140, retro_mmul_1635, retro_mmul_1947,
Monodelphis domestica	ENSMODG00000003897	1 retrocopy	retro_mdom_271,
Mus musculus	ENSMUSG00000018362	1 retrocopy	retro_mmus_229,
Pongo abelii	ENSPPYG00000008569	1 retrocopy	retro_pabe_3501,
Rattus norvegicus	ENSRNOG00000015329	1 retrocopy	retro_rnor_42,
Sarcophilus harrisii	ENSSHAG00000011391	1 retrocopy	retro_shar_165,
Tupaia belangeri	ENSTBEG00000006274	14 retrocopies	retro_tbel_1635, retro_tbel_2077, retro_tbel_2672, retro_tbel_2792, retro_tbel_290, retro_tbel_3638, retro_tbel_4120 , retro_tbel_4358, retro_tbel_4414, retro_tbel_4435, retro_tbel_4558, retro_tbel_810, retro_tbel_97, retro_tbel_976,
Tupaia belangeri	ENSTBEG00000009007	3 retrocopies	retro_tbel_1475, retro_tbel_3862, retro_tbel_3962,