RetrogeneDB ID: retro_tbel_1029

Retrocopy location

• Organism: Treeshrew (Tupaia belangeri)
• Coordinates: GeneScaffold_3619:102188..103794(-)
• Located in intron of: ENSTBEG00000014310

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSTBEG00000013569
• Aliases: None
• Description: None

Sequence

>retro_tbel_1029
ATGAAGCAGAGTTCGAACGTGCCGGCCTTCCTCAGCAAGCTGTGGAGGCTTGTAGAAGAAACCCACACCAACGAGTTTAT
CACCTGGAGCCAGAATGGCCAAAGTTTTCTGGTCTTGGATGAACAAAGGTTTGCAAAAGAAATTCTTCCCAAGTACTTCA
AGCACAATAACATGGCAAGCTTTGTGAGGCAGCTGAATATGCATGGTTTCCGTAAAGTAGTACATATTGACTCTGGAATT
GTAAAGCAGGAAAGAGATGGTCCTGTTGAATTTCAGCATCCTTACTTCAAACAAGGCCAGGATGACTTGTTAGAGAACAT
TAAAAGGAAGGTTTCATCTTCAAAACCAGAAGAAAATAAAATTCGTCAGGAAGATTTAACAAAAATTATAAGTAGTGCTC
AGAAGGTTCAAATAAAACAAGAAACTATTGAATCCAGGCTTTCTGAATTAAAAAGTGAGAATGAGTCCCTTTGGAAAGAA
GTATCAGAGTTACGGGCAAAACATGCAACAACAACAAGTTATTCGAAAGATTGTCCAGTTTATTGTTACATTGGTTCAGA
ATAACCAGCTTGTGAGTTTAAAACGTAAAAGGCCTCTACTTCTGAATACTAATGGAGCCCAAAAGAAGAATCTGTTTCAA
CACATAGTCAAAGAACCAACTGATAATCACCATCATAAAGTTCCACACAGTAGGACTGAAGGTTTAAAGCCAAGAGAACG
GATTTCAGATGACATCATTATTTATGATGTTACTGACGATAACGCGGATGAAGAAAATATCCCAGTTATTCCAGAAACAA
ATGAGGATGTTATATCTGATCCCTCCAGTTGTAGCCAGTACCCTGATATTGTCATTGTTGAAGATGACAATGAAGATGAA
TATGCACCTGTTATTCAGAGTGGAGATCAGAGTGAACCAGCCAGAGAATCCCTAAGTTCAGGCAGTGATTGCACCAGCCC
ACTCATGTCTAGTGCTGTCCAGCTAAATGGCTCATCCAGCTTGACCACAGAAGATCCTGTGACCATGATGGATTCTATAT
TGAATGATAACTTTAATCTCTTGGGAAAGGTTGAGCTGTTGGATTATCTTGACAGTATTGATTGCAGTTTAGAGGACTTC
CAAGCCATGCTGTCAGGAAGACAGTTTAGCATAGACCCAGATCTCCTGGTTGATCTTTTCACTAGTTCTGTGCAGATGAA
TCCCACAGATTACATCAATAATACAAAATCTGAGAATAAAGGATTAGAAACCTCCAAGAACAATGTAGTTCAGCCAACTT
CAGAAGAGGGAAGAAAATCTAAATCCAAACCAGATAAGCAGCTTATCCAGTACACTGCTTTTCTACTTCTTGCATTCCTC
GATGGGAACCCTGCTTCCACTGTTGAACAGGGGGGTACACCAGCATCATCAGAAGCTATGTCCTCTGTAGATAAACCCAT
AGAAGTTGATGAGCTTCTGGATAGCAGCCTGGACCCAGAACCAACCCAGAGTAAGCTCGTTCGCCTAGAGCCATTGACTG
AAGCTGAAGCTAGTGAAGCTACACTGTTTTATTTATGTAAACTTGCTCCCGCACCTCTGGATAGTGATATGCCACTTTTA
GATAGC

Alignment

ORF - retro_tbel_1029 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 98.14 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MKQSSNVPAFLSKLWTLVEETHTNEFITWSQNGQSFLVLDEQRFAKEILPKYFKHNNMASFVRQLNMYGF
          MKQSSNVPAFLSKLW.LVEETHTNEFITWSQNGQSFLVLDEQRFAKEILPKYFKHNNMASFVRQLNM.GF
Retrocopy MKQSSNVPAFLSKLWRLVEETHTNEFITWSQNGQSFLVLDEQRFAKEILPKYFKHNNMASFVRQLNMHGF

Parental  RKVVHIDSGIVKQERDGPVEFQHPYFKQGQDDLLENIKRKVSSSKPEENKIRQEDLTKIISSAQKVQIKQ
          RKVVHIDSGIVKQERDGPVEFQHPYFKQGQDDLLENIKRKVSSSKPEENKIRQEDLTKIISSAQKVQIKQ
Retrocopy RKVVHIDSGIVKQERDGPVEFQHPYFKQGQDDLLENIKRKVSSSKPEENKIRQEDLTKIISSAQKVQIKQ

Parental  ETIESRLSELKSENESLWKEVSELRAKHA-QQQQVIRKIVQFIVTLVQNNQLVSLKRKRPLLLNTNGAQK
          ETIESRLSELKSENESLWKEVSELRAKHA.QQ.QVIRKIVQFIVTLVQNNQLVSLKRKRPLLLNTNGAQK
Retrocopy ETIESRLSELKSENESLWKEVSELRAKHA>QQ-QVIRKIVQFIVTLVQNNQLVSLKRKRPLLLNTNGAQK

Parental  KNLFQHIVKEPTDNHHHKVPHSRTEGLKPRERISDDIIIYDVTDDNADEENIPVIPETNEDVISDPSGCS
          KNLFQHIVKEPTDNHHHKVPHSRTEGLKPRERISDDIIIYDVTDDNADEENIPVIPETNEDVISDPS.CS
Retrocopy KNLFQHIVKEPTDNHHHKVPHSRTEGLKPRERISDDIIIYDVTDDNADEENIPVIPETNEDVISDPSSCS

Parental  QYPDIVIVEDDNEDEYAPVIQSGDQSEPARESLSSGSDCTSPLMSSAVQLNGSSSLTTEDPVTMMDSILN
          QYPDIVIVEDDNEDEYAPVIQSGDQSEPARESLSSGSDCTSPLMSSAVQLNGSSSLTTEDPVTMMDSILN
Retrocopy QYPDIVIVEDDNEDEYAPVIQSGDQSEPARESLSSGSDCTSPLMSSAVQLNGSSSLTTEDPVTMMDSILN

Parental  DNINLLGKVELLDYLDSIDCSLEDFQAMLSGRQFSIDPDLLVDLFTSSVQMNPTDYINNTKSENKGLETS
          DN.NLLGKVELLDYLDSIDCSLEDFQAMLSGRQFSIDPDLLVDLFTSSVQMNPTDYINNTKSENKGLETS
Retrocopy DNFNLLGKVELLDYLDSIDCSLEDFQAMLSGRQFSIDPDLLVDLFTSSVQMNPTDYINNTKSENKGLETS

Parental  KNNVVQPASEEGRKSKSKPDKQLIQYTAFPLLAFLDGNPASTVEQGGTPASSEAMSSVDNPIEVDELLDS
          KNNVVQP.SEEGRKSKSKPDKQLIQYTAF.LLAFLDGNPASTVEQGGTPASSEAMSSVD.PIEVDELLDS
Retrocopy KNNVVQPTSEEGRKSKSKPDKQLIQYTAFLLLAFLDGNPASTVEQGGTPASSEAMSSVDKPIEVDELLDS

Parental  SLDPEPTQSKLVRLEPLTEAEASEATLFYLCELAPAPLDSDMPLLDS
          SLDPEPTQSKLVRLEPLTEAEASEATLFYLC.LAPAPLDSDMPLLDS
Retrocopy SLDPEPTQSKLVRLEPLTEAEASEATLFYLCKLAPAPLDSDMPLLDS

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_1029 retrocopy.

TSS

Tupaia belangeri was not studied using FANTOM5 data.

Lab

retro_tbel_1029 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 4 parental genes, and 6 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000010951	1 retrocopy	retro_chof_621,
Cavia porcellus	ENSCPOG00000007509	1 retrocopy	retro_cpor_1341,
Macaca mulatta	ENSMMUG00000007910	1 retrocopy	retro_mmul_867,
Tupaia belangeri	ENSTBEG00000013569	3 retrocopies	retro_tbel_1029 , retro_tbel_19, retro_tbel_3,