RetrogeneDB ID: retro_tbel_3879

Retrocopy location

• Organism: Treeshrew (Tupaia belangeri)
• Coordinates: scaffold_2648:51442..52589(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSTBEG00000007668
• Aliases: None
• Description: None

Sequence

>retro_tbel_3879
TGCATAATGGACTATCAGAATAAAGGAAAGACCTCAGAGTGTTCTCAGTATCAGCAGATGTTGCATACAAACTTGGTATA
CCTTGCTACAATAGCAGATTCTAGTCAAAATATGCAGTCTCTTTTACCAGCACCACCAACACAGAATATGCCTATGGGTC
CTGGAGGAATGAATGAGTGGCCCTCCCCCACCTCCACGCTCTCACAACATGCCTTCAGATGGAATGGTAGGTGGGGGTCC
TCCTGCACCACACATGCAGAACCAGATGAACGGCCAGATGCCTGGACCTAATCATATGCCTATGCAGGGACCTGGACCCT
ATCAATTCAATATGACAAATAGTTCTATGAATATGCCTTCAAGTAGCCATGGATCCATGGGAGGTTACAACCATTGCGTG
CCATCATCACAGAGCATGCCCATACAGAATCAGATGACAATGAGTCAAGGACAACCTATGGGAAACTATGGCCCCAGGCC
AAATATGAATATGCAACCAAACCAAGGCCCGATGATGCATCAACAGCCTCCTTCTCAGCAATACAATATGCCACAGGGAG
GCGGGCAGCATAACCAAGGACAGCAACCACCTATGGGGATGATGGGTCAAGTTAACCAAGGCAGTCACATGACGGGTCAG
AGACAGATTCCTCCTTATAGACCACCTCAACAGGACCCACCACAGCAGTACTCAGGCCAGGAAGACTATTATGGGGACCA
ATACGGTCATGGTGGACAAGGTCCTCCAGAAGGCATGAACCAGCAATATTACCCTGATGGTCATAATGATTACGGTTATC
AGCAACCGTCGTATCCTGAACAAGGCTACGATAGGCCTTATGAGGATTCCTCACAACATTACTACGAAGGAAGAAATTCT
CAGTATGGCCAGCAGCAAGATGCTTACCAAGGACCACCTCCCCAACAGGGATATCCACCCCAACAGCAGCAGTACCCAGG
GCAGCAGGGCTATCCAGGATAACAACAGGGTTACGGTCCTTCTCAAGGGGGTCCAGGTCCTCAGTATCCTAACTATCCAC
AGGGACAAGGTCAACAGTATGGGGGATATAGACCAACACAGCCTGGACCACCACAGCCACCCCAGCAGAGACCTTATGGA
TACGATCAGGGGCAGTACGGAAATTAC

Alignment

ORF - retro_tbel_3879 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 90.36 %
• Parental protein coverage: 96.94 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  CIMDYQNKGKTSECS-YQQM-HTN-VYLATIADSNQNMQSLLPAPPTQNMPMGPGGMNQ-SGPPPPPRSH
          CIMDYQNKGKTSECS.YQQM.HTN.VYLATIADS.QNMQSLLPAPPTQNMPMGPGGMN....PP.PPRSH
Retrocopy CIMDYQNKGKTSECSQYQQMLHTNLVYLATIADSSQNMQSLLPAPPTQNMPMGPGGMNE>GPPP-PPRSH

Parental  NMPSDGMVGGGPPAPHMQNQMNGQMPGPNHMPMQGPGPNQLNMTNSSMNMPSSSHGSMGGYNHSVPSSQS
          NMPSDGMVGGGPPAPHMQNQMNGQMPGPNHMPMQGPGP.Q.NMTNSSMNMPSSSHGSMGGYNH.VPSSQS
Retrocopy NMPSDGMVGGGPPAPHMQNQMNGQMPGPNHMPMQGPGPYQFNMTNSSMNMPSSSHGSMGGYNHCVPSSQS

Parental  MPVQNQMTMSQGQPMGNYGPRPNMNMQPNQGPMMHQQPPSQQYNMPQGGGQHYQGQQPPMGMMGQVNQGS
          MP.QNQMTMSQGQPMGNYGPRPNMNMQPNQGPMMHQQPPSQQYNMPQGGGQH.QGQQPPMGMMGQVNQGS
Retrocopy MPIQNQMTMSQGQPMGNYGPRPNMNMQPNQGPMMHQQPPSQQYNMPQGGGQHNQGQQPPMGMMGQVNQGS

Parental  HMMGQRQIPPYRPPQQGPPQQYSGQEDYYGDQYSHGGQGPPEGMNQQYYPDXXXXXXXXXXXXXXXXXXR
          HM.GQRQIPPYRPPQQ.PPQQYSGQEDYYGDQY.HGGQGPPEGMNQQYYPD..................R
Retrocopy HMTGQRQIPPYRPPQQDPPQQYSGQEDYYGDQYGHGGQGPPEGMNQQYYPDGHNDYGYQQPSYPEQGYDR

Parental  PYEDSSQHYYEGGNSQYGQQQDAYQGPPPQQGYPPQQQQYPGQQGYPGQQQGYGPSQGGPGPQYPNYPQG
          PYEDSSQHYYEG.NSQYGQQQDAYQGPPPQQGYPPQQQQYPGQQGYPG.QQGYGPSQGGPGPQYPNYPQG
Retrocopy PYEDSSQHYYEGRNSQYGQQQDAYQGPPPQQGYPPQQQQYPGQQGYPG*QQGYGPSQGGPGPQYPNYPQG

Parental  QGQQYGGYRPTQPGPPQPPQQRPYGYDQGQYGNY
          QGQQYGGYRPTQPGPPQPPQQRPYGYDQGQYGNY
Retrocopy QGQQYGGYRPTQPGPPQPPQQRPYGYDQGQYGNY

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_3879 retrocopy.

TSS

Tupaia belangeri was not studied using FANTOM5 data.

Lab

retro_tbel_3879 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 3 parental genes, and 5 retrocopies.

Species	Parental gene accession	Retrocopies number
Mus musculus	ENSMUSG00000037013	1 retrocopy	retro_mmus_1951,
Ictidomys tridecemlineatus	ENSSTOG00000015699	1 retrocopy	retro_itri_1194,
Tupaia belangeri	ENSTBEG00000007668	3 retrocopies	retro_tbel_3879 , retro_tbel_4107, retro_tbel_8,