RetrogeneDB ID: retro_tbel_4436

Retrocopy location

• Organism: Treeshrew (Tupaia belangeri)
• Coordinates: scaffold_83260:221..1341(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: CKAP2L
• Ensembl ID: ENSTBEG00000013625
• Aliases: None
• Description: cytoskeleton associated protein 2-like [Source:HGNC Symbol;Acc:26877]

Sequence

>retro_tbel_4436
GAACAGCAGAGAAAACTCCAAGAATACCTTGCAGCCAAGGGAAAACTAAAGAACCAAAACACCAAGCCTTATCTAAAAGC
CAAGAATTACTGCCCGAATCCACCACCTCCTAAATCTACTATTAGACCCAAAAAAGGATGTTACTCGCCATGTTGTCTTG
CCTGTCAAAACCACACAGCCCGTTAGCATTAAACTCCAGCCCAGAACAGCCAATATCACAGGGTCACAGAAGCCAAAGTT
GGAGCCACCAAAACTTGTGGGCAAAGGGCTGACTTCAGGATGTGTTTCTTTGATGCCAAATGGTAAGTATTCCAGCAGGA
CTCATCAGCTGCATGAAGGTGGATCATCCACTGCAGGAGAACTGTCAAGAAAACCTGTGGGGTTACTCAATATACAGGAA
TTGAAACCTATAAAGCAGCAAGTAACAGATCAAGGAAATGCTAAATGTATAGACTCTGTGGACAGTACCTGTGTTGAAAA
CCAATCTTCGGATATCTTTTTGAAAGAGATGAACAAAGAGAACTTGTCCCAAACCTTATTAGAACCTGAGAGGAAGCCAG
ATCCTGAATCATGTGCCATAACTAAGACAAAGACTAACTCTCATAATCCAATCAAGGGAAGTTTGGCTCCTAAACAAGCC
ATGGGCAAAAGTTCAGTGAATAGTGCTGTTCTTAAAGACAGAGTTAATAAGCAACTTGTTGGAGAAACACAAATCAGGAC
TCTACCAGTAAAGTCACAGCAACTGTCTAAAGGAGCAGGTCTTACAAGACCAAGAGAAAAACACTGAAGAACAATTCCCT
CTCACCATATTCAGACCTTTAATAGGACTCAAGTATTAAAGAAGCCAGTGGTCAAGGACATAAAGGTTAGTAGGAGTAAA
TACAAAGAACCAAAAGAAACTAAGTCACAGTCATACCTTGCTAATGAACAGAAAGTAAAAACTTCTAAACCCAGAATATA
CCCCAATTTGCCTCAGAGTGAGTATGGTAACAAACATCCAAATGCGAAGGAAAATCAGAAGTCCACTCAACCTTATTTTA
GACCTCCAATATCATGTGTACTTCAGAGTTCAAAAGCCATAAGCCAGAGGTCTCATCTGACAACTGCCAACTTTAATTCA

Alignment

ORF - retro_tbel_4436 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 94.12 %
• Parental protein coverage: 51.31 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  ERQRKLQEYLAAKGKLKNQNTKPYLKAKNNCPNPPPPKSTIRPKK-DVTRHVVLPVKTTQPISIKLQPRT
          E.QRKLQEYLAAKGKLKNQNTKPYLKAKN.CPNPPPPKSTIRPKK.DVTRHVVLPVKTTQP.SIKLQPRT
Retrocopy EQQRKLQEYLAAKGKLKNQNTKPYLKAKNYCPNPPPPKSTIRPKK>DVTRHVVLPVKTTQPVSIKLQPRT

Parental  ANITGSQKPKLEPPKLVGKGLTSGCVSSMPNGKRSSRTHHLHEGGSSTAGELSRKPVGLLNMQELKPIKQ
          ANITGSQKPKLEPPKLVGKGLTSGCVS.MPNGK.SSRTH.LHEGGSSTAGELSRKPVGLLN.QELKPIKQ
Retrocopy ANITGSQKPKLEPPKLVGKGLTSGCVSLMPNGKYSSRTHQLHEGGSSTAGELSRKPVGLLNIQELKPIKQ

Parental  QVTDQGNAKCIDSVDSTHVENQSSDIFLKEMNKENLPQTLLEPERKPDPESCAITKTKTNSHNPIKGSLA
          QVTDQGNAKCIDSVDST.VENQSSDIFLKEMNKENL.QTLLEPERKPDPESCAITKTKTNSHNPIKGSLA
Retrocopy QVTDQGNAKCIDSVDSTCVENQSSDIFLKEMNKENLSQTLLEPERKPDPESCAITKTKTNSHNPIKGSLA

Parental  PKQAMGKSSVNSAVLKDRVNKQLVGETQIRTLPVKSQQLSKGAGLTRPGEKHARTVPSHHIQTFNRTQVL
          PKQAMGKSSVNSAVLKDRVNKQLVGETQIRTLPVKSQQLSKGAGLTRP.EKH.RT.PSHHIQTFNRTQVL
Retrocopy PKQAMGKSSVNSAVLKDRVNKQLVGETQIRTLPVKSQQLSKGAGLTRPREKH*RTIPSHHIQTFNRTQVL

Parental  KKPVVKDIKVSRSKYKELKETKSQSYLVNEQKVKTSKPRVYPSLPQSEYGNKHPNVKENQKSTQPYFRPP
          KKPVVKDIKVSRSKYKE.KETKSQSYL.NEQKVKTSKPR.YP.LPQSEYGNKHPN.KENQKSTQPYFRPP
Retrocopy KKPVVKDIKVSRSKYKEPKETKSQSYLANEQKVKTSKPRIYPNLPQSEYGNKHPNAKENQKSTQPYFRPP

Parental  TSCALQRSKAISQRSHLTTAKFNS
          .SC.LQ.SKAISQRSHLTTA.FNS
Retrocopy ISCVLQSSKAISQRSHLTTANFNS

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_4436 retrocopy.

TSS

Tupaia belangeri was not studied using FANTOM5 data.

Lab

retro_tbel_4436 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 7 parental genes, and 9 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000007242	1 retrocopy	retro_cfam_858,
Cavia porcellus	ENSCPOG00000010435	2 retrocopies	retro_cpor_229, retro_cpor_528,
Felis catus	ENSFCAG00000028904	1 retrocopy	retro_fcat_615,
Mustela putorius furo	ENSMPUG00000009729	1 retrocopy	retro_mputfur_1172,
Ochotona princeps	ENSOPRG00000012796	1 retrocopy	retro_opri_904,
Tupaia belangeri	ENSTBEG00000005807	1 retrocopy	retro_tbel_176,
Tupaia belangeri	ENSTBEG00000013625	2 retrocopies	retro_tbel_1637, retro_tbel_4436 ,