RetrogeneDB ID: retro_tbel_4107

Retrocopy location

• Organism: Treeshrew (Tupaia belangeri)
• Coordinates: scaffold_67540:816..2001(+)
• 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_4107
ATGCTGGATGAAAATAACCATCTTATTCAGTGCATAATGGACTATCAGAATAAAGGAAAGACCTCAGAGTGTTCTCAGTA
TCAGCAGATGTTGCATACAAACTTGGTATACCTTGCTACAATAGCAGATTCTAATCAAAATATGCAGTCTCTTTTACCAG
CACCACCCACACAGAATATGCCTATGGGTCCTGGAGGGATGAATCAGAGTGGCCCTCCCCCACCTCCACACTCTCACAAC
ATGCCTTCAGATGGAATGGTAGGTGGGGGTCCTCCTGCACCACACATGCAGAACCAGATGAACGGCCAGATGCCTGGACC
TAACCATATGCCTATGCAGGGACCTGGACCCAATCAACTCAATATGACAAATAGTTCTATGAATATGCCTTCAAGTAGCC
ATGGATCCATGGGAGGTTACAACCATTCCGTGCCATCATCACAGAGCATGCCCGTACAGAATCAGATGACAATGAGTCAA
GGACAACCTATGGGAAACTATGGCCCCAGGCCAAATATGAATATGCAACCAAACCAAGGCCCGATGATGCATCAGCAGCC
TCCTTCTCAGCAATACAATATGCCACAGAGAGGCGGGCAGCATTACTAAGGACAGCAACCACCTATGGGGATGATGGGTC
AAGTTAACCAAGGCAGTCACATGATGGGTCAGAGACAGATTCCTTCCTATAGACCACCTCAACAGGGCCCACCACAGCAG
TACTCAGGCCAGGAAGACTATTATGGGGACCAATACAGTCATGGTGGACAAGGTCCTCCAGAAAGCATGAACCAGCAATA
TTACCCTGATGGTCATAATGATTACGGTTATCAGCAACCGTCGTATCCTGAACAAGGCTACAATAGGCCTTATGAGGATT
CCTCACAACATTACTATGAAGGAGGAAATTCTCAGTATGGCCAGCAGCAAGATGCTTACCAAGGACCACCTCCCCAACAG
GGATATCCACCCCAACAGCAGCAGTACCCAGGGCAGCAGGGCTATCCAGGACAACAACAGGGTTACGGTCCTTCTCAAGG
GGGTCCAGGTCCTCAGTATCTTAACTATCCACAGGGACAAGGTCAACAGTATGGGGGTTATAGACCAACACAGCCTGGAC
CACCACAGCCACCCCAGCAGAGGCCTTACGGATACGATCAGGGGCAGTACGGAAATTACCAACAG

Alignment

ORF - retro_tbel_4107 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 93.16 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MLDENNHLIQCIMDYQNKGKTSECS-YQQM-HTN-VYLATIADSNQNMQSLLPAPPTQNMPMGPGGMNQS
          MLDENNHLIQCIMDYQNKGKTSECS.YQQM.HTN.VYLATIADSNQNMQSLLPAPPTQNMPMGPGGMNQS
Retrocopy MLDENNHLIQCIMDYQNKGKTSECSQYQQMLHTNLVYLATIADSNQNMQSLLPAPPTQNMPMGPGGMNQS

Parental  GPPPPPRSHNMPSDGMVGGGPPAPHMQNQMNGQMPGPNHMPMQGPGPNQLNMTNSSMNMPSSSHGSMGGY
          GPPPPP.SHNMPSDGMVGGGPPAPHMQNQMNGQMPGPNHMPMQGPGPNQLNMTNSSMNMPSSSHGSMGGY
Retrocopy GPPPPPHSHNMPSDGMVGGGPPAPHMQNQMNGQMPGPNHMPMQGPGPNQLNMTNSSMNMPSSSHGSMGGY

Parental  NHSVPSSQSMPVQNQMTMSQGQPMGNYGPRPNMNMQPNQGPMMHQQPPSQQYNMPQGGGQHYQGQQPPMG
          NHSVPSSQSMPVQNQMTMSQGQPMGNYGPRPNMNMQPNQGPMMHQQPPSQQYNMPQ.GGQHY.GQQPPMG
Retrocopy NHSVPSSQSMPVQNQMTMSQGQPMGNYGPRPNMNMQPNQGPMMHQQPPSQQYNMPQRGGQHY*GQQPPMG

Parental  MMGQVNQGSHMMGQRQIPPYRPPQQGPPQQYSGQEDYYGDQYSHGGQGPPEGMNQQYYPDXXXXXXXXXX
          MMGQVNQGSHMMGQRQIP.YRPPQQGPPQQYSGQEDYYGDQYSHGGQGPPE.MNQQYYPD..........
Retrocopy MMGQVNQGSHMMGQRQIPSYRPPQQGPPQQYSGQEDYYGDQYSHGGQGPPESMNQQYYPDGHNDYGYQQP

Parental  XXXXXXXXRPYEDSSQHYYEGGNSQYGQQQDAYQGPPPQQGYPPQQQQYPGQQGYPGQQQGYGPSQGGPG
          ........RPYEDSSQHYYEGGNSQYGQQQDAYQGPPPQQGYPPQQQQYPGQQGYPGQQQGYGPSQGGPG
Retrocopy SYPEQGYNRPYEDSSQHYYEGGNSQYGQQQDAYQGPPPQQGYPPQQQQYPGQQGYPGQQQGYGPSQGGPG

Parental  PQYPNYPQGQGQQYGGYRPTQPGPPQPPQQRPYGYDQGQYGNYQQ
          PQY.NYPQGQGQQYGGYRPTQPGPPQPPQQRPYGYDQGQYGNYQQ
Retrocopy PQYLNYPQGQGQQYGGYRPTQPGPPQPPQQRPYGYDQGQYGNYQQ

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_4107 retrocopy.

TSS

Tupaia belangeri was not studied using FANTOM5 data.

Lab

retro_tbel_4107 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,