RetrogeneDB ID: retro_tbel_4088

Retrocopy location

• Organism: Treeshrew (Tupaia belangeri)
• Coordinates: scaffold_66838:5708..6722(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSTBEG00000014283
• Aliases: None
• Description: None

Sequence

>retro_tbel_4088
AACAGTCAGCAACAAGTAGAGAATGAGCCTGCTGGTCATGTCACCAAGACGAGGAGGAGGTGCAAGGTGTTGTGTGGGGA
TTCTCACCCCCAGCAGGATCATTTAGAGATAAAAATAAGTGATCCTACTGAATTCCAGAATCGAAAACCAGGATCTCAGA
ACTACAACTGAAGTTGCTTCTCTATCAGATGAGAGCCAAGCACTGGAGAATACAGAATCCTCAGGGAAGAGTGGAATTCA
CGGTAAAAAAGATTCAAAGGTACCTTCAGGAAAGAAGTCTGTCTGCCCAGAGGGGCTTTCCAAACATGGAAAAAACAAAA
GAAACGCAAACACTACTCCAAACTTTAAGAAGCTTCATGAGGCTCGTTTCAAGGAAATGGAATCCATTGATCAATATATT
GAGAGAAAAAAGAAACATTTTGAAGAACACAATTCATTCAATGAACTGAAGAAGTAGCTCATGAGTAAGGGAGGGGTAGT
GACTCCCGTTCATCCAAGAAGACCCTCTGTGGCTTGCACACCCGTCAGCCAGCGGCGCTCACAAGGCCGGTCTCAGGGCC
TCACAAGTCAAAGCACCTTGTGTCTGAAGGGGTCGATCAGACGCTCAGCCCTCTCAACAACTAAAATTAAAGTCAGGTTC
TCGGCTGCTACTAAGGATAACGAGCACAAACGTTCCCTGACCAAGACTCCAGCCAGGAAGTCTCCACACGTGATTGTATC
TGGGAGTACCCCAAAAGGCCAGGCTGTGCTTGAGTCACACAAGTTCAAGGTAACTGGGAGGAATTCTGCTGCTGTTATCA
CACCATTCAAGTTGACAACTGAGGCATCGCAGACTCTAGTCTCCATTAAGAAACCAGTGTTTGATCTGAAAGCAAGTTTG
TCTCGTCCTCTCAACTATGACCCAGCAAAGGAAAGCTGAAACCATGGGGGCAATCTAAAGAAGATAATTCTCTGAGTGAA
CATGGAAACAGAGTTACCTTCCACAAGAAAACTTACAAACAGCCTCATCTCCAG

Alignment

ORF - retro_tbel_4088 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 81.52 %
• Parental protein coverage: 82.31 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  DSQQQAENEPAGHVTKTRRRCKELCGDSHPQQDHLEIKISDPTEFQNQRKENQDLR-TTTEVASLSDESQ
          .SQQQ.ENEPAGHVTKTRRRCK.LCGDSHPQQDHLEIKISDPTEFQN.....Q............S....
Retrocopy NSQQQVENEPAGHVTKTRRRCKVLCGDSHPQQDHLEIKISDPTEFQNRKPGSQNYN>EVASLSDESQALE

Parental  AQENTESSG---EKDSKVPSGKKKSVYPDGLSKPGKNKRTANTTPXXXXXXXXXFKEMESIDQYIERKKK
          ..E....SG....KDSKVPSG.KKSV.P.GLSK.GKNKR.ANTTP.........FKEMESIDQYIERKKK
Retrocopy NTESSGKSGIHGKKDSKVPSG-KKSVCPEGLSKHGKNKRNANTTPNFKKLHEARFKEMESIDQYIERKKK

Parental  HFEEHNSFNELKKQPMSKGGVVTPVHPRRPSVACTPVSQRRSQGRSQGLTSQSTLCLKGSIRRSALSTTK
          HFEEHNSFNELKK..MSKGGVVTPVHPRRPSVACTPVSQRRSQGRSQGLTSQSTLCLKGSIRRSALSTTK
Retrocopy HFEEHNSFNELKK*LMSKGGVVTPVHPRRPSVACTPVSQRRSQGRSQGLTSQSTLCLKGSIRRSALSTTK

Parental  MNVRFSAATKDNEHKRSLTKTPARKSPHVIVSGSTPKGQAVLESHKFKATGRNSAAALTPFKLTAEALQT
          ..VRFSAATKDNEHKRSLTKTPARKSPHVIVSGSTPKGQAVLESHKFK.TGRNSAA..TPFKLT.EA.QT
Retrocopy IKVRFSAATKDNEHKRSLTKTPARKSPHVIVSGSTPKGQAVLESHKFKVTGRNSAAVITPFKLTTEASQT

Parental  PVSNKKPVFDLKASLSRPLNYE-PHKGKLKPWGQSKE-NSLSEHGNRVTFHKKTYKQPHLQ
          .VS.KKPVFDLKASLSRPLNY..P.KGKLKPWGQSKE.NSLSEHGNRVTFHKKTYKQPHLQ
Retrocopy LVSIKKPVFDLKASLSRPLNYD<PSKGKLKPWGQSKEDNSLSEHGNRVTFHKKTYKQPHLQ

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_4088 retrocopy.

TSS

Tupaia belangeri was not studied using FANTOM5 data.

Lab

retro_tbel_4088 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 8 parental genes, and 10 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000010774	1 retrocopy	retro_btau_1714,
Canis familiaris	ENSCAFG00000009538	3 retrocopies	retro_cfam_1685, retro_cfam_2137, retro_cfam_578,
Cavia porcellus	ENSCPOG00000012875	1 retrocopy	retro_cpor_993,
Cavia porcellus	ENSCPOG00000020956	1 retrocopy	retro_cpor_258,
Myotis lucifugus	ENSMLUG00000009782	1 retrocopy	retro_mluc_389,
Mustela putorius furo	ENSMPUG00000008844	1 retrocopy	retro_mputfur_1626,
Otolemur garnettii	ENSOGAG00000034763	1 retrocopy	retro_ogar_3125,
Tupaia belangeri	ENSTBEG00000014283	1 retrocopy	retro_tbel_4088 ,