RetrogeneDB ID: retro_tbel_4240

Retrocopy location

• Organism: Treeshrew (Tupaia belangeri)
• Coordinates: scaffold_72901:19870..20992(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: GFAP
• Ensembl ID: ENSTBEG00000011873
• Aliases: None
• Description: glial fibrillary acidic protein [Source:HGNC Symbol;Acc:4235]

Sequence

>retro_tbel_4240
CTGCAGGCCTCAGTGGACTTCTCGCTGGCTGACGCCATCAACACCGAGTTCAAGAACACTCACACCAATGAGAAAGTGGA
GCTGCAGGAACTGAATGACTGATTCGCCAACTACATCGACAAGGTGTGCTTCTTGGAGCAGCAGAACAAGATCCTGATGG
CCGAGCTCAAGCAGCTCAAGGGCCAGAGCAAGTCGTGCCTGGGGGACCTCTATGAGGAGGAGATGCGGGAGCTGCACAGG
CAGGTGGATAAGCTCACCAACGAGAAGGCCCACGTGGAGGTGGAGCGTGACAACCTGGCCAAGGACATCATGAGGCTTTG
GGAGAAATTGCAGGAGGAGATGCTTCAGAGAGAGGAAGCTGAAAGCACTCTGCAATCTTTCAGACAGGATGTTGACAATG
CTTCTTTGGCACGTCTTGACCTTGAGCACAAAGTGGAGTCCTTGCAAGAAGAGATTGCCTTTTTGAAGAAACTACACAAA
GAGGAAATTCAGTAGCTGCAAGCCCAGATTCAGGAACAGCATGTCCAAGTTGATATGGATGTTTCCAAGACTGACCTCAC
GGCTGCCCTGCATGATGTCTGTCAGCAGTATGAAAGTGTAGCTGCCAAGAACCTTCAGGAGGCAGAAGAATGGTACAAGT
CCAAGTTTGCTGACCTCTCAGAAGCTGCTAACCACAACAACGATGCCCTGTGCCAGGCGAAGCAGGAGTCCAATGAGTAC
TGGCGGCAGGTGCAGTCCCTCACCTATGAAGTGGATGTGCTTAAAGGAACTAATGAATCTCTGGAATGCCAGATGTGTGA
AATGGCAGAGAACTTTGCTGTCGAAGCTGCTAACTACCAAGACACCACTGGCCACCTGCAGGATGAGATTCAGAACATGA
AGGAAGAAATGGCTCGCCACCTTCGTGAATACCAGGACCTGCTCAATGTTAAGATGGCTCTTGACATTGAGATTGCCACC
TACAGGAAGCTGCTGGAAGGCGAGGAAAGCAGGATTTCTCTGCCTCTTCCAAACTTCTCCTCCCTGAATCTGAGGGACAC
TAATCTGGATTCACTCCCTCTGGTTGACACCCACCCAAAAAGAACACTTCTGATTAAGACGGTTAAAACTAGTGATGGAC
AG

Alignment

ORF - retro_tbel_4240 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 56.15 %
• Parental protein coverage: 90.34 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  LPARVDFSLAGALNAGFKETRASERAEMMELNDRFASYIEKVRFLEQQNKALAAELNQLRAKEPTKLADV
          L.A.VDFSLA.A.N..FK.T...E..E..ELND.FA.YI.KV.FLEQQNK.L.AEL.QL.......L.D.
Retrocopy LQASVDFSLADAINTEFKNTHTNEKVELQELND*FANYIDKVCFLEQQNKILMAELKQLKGQSKSCLGDL

Parental  YQAELRELRLRLDQLTANSARLEVERDNLAQDLTTLRQKLQDETNLRMEAENNLAAYRQEADEATLARLD
          Y..E.REL....D.LT...A..EVERDNLA.D...L..KLQ.E...R.EAE..L...RQ..D.A.LARLD
Retrocopy YEEEMRELHRQVDKLTNEKAHVEVERDNLAKDIMRLWEKLQEEMLQREEAESTLQSFRQDVDNASLARLD

Parental  LERKTESLEEEIQFLRKIHEEEVRELQEQLARQQVHVELDVAKPDLTAALREIRTQYEAMASSNMHEAEE
          LE.K.ESL.EEI.FL.K.H.EE...LQ.Q...Q.V.V..DV.K.DLTAAL.....QYE..A..N..EAEE
Retrocopy LEHKVESLQEEIAFLKKLHKEEIQ*LQAQIQEQHVQVDMDVSKTDLTAALHDVCQQYESVAAKNLQEAEE

Parental  WYRSKFADLTDAAARNAELLRQAKHEANDYRRQLQALTCDLESLRGTNESLERQMREQEERHAREAASYQ
          WY.SKFADL..AA..N...L.QAK.E.N.Y.RQ.Q.LT.....L.GTNESLE.QM.E..E..A.EAA.YQ
Retrocopy WYKSKFADLSEAANHNNDALCQAKQESNEYWRQVQSLTYEVDVLKGTNESLECQMCEMAENFAVEAANYQ

Parental  EALARLEEEGQSLKDEMARHLQEYQELLNVKLALDIEIATYRKLLEGEENRITIPVQTFSNLQIRETSLD
          .....L..E.Q..K.EMARHL.EYQ.LLNVK.ALDIEIATYRKLLEGEE.RI..P...FS.L..R.T.LD
Retrocopy DTTGHLQDEIQNMKEEMARHLREYQDLLNVKMALDIEIATYRKLLEGEESRISLPLPNFSSLNLRDTNLD

Parental  TKSVSEGHLKRNIVVKTVEMRDGE
          .......H.KR....KTV...DG.
Retrocopy SLPLVDTHPKRTLLIKTVKTSDGQ

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_4240 retrocopy.

TSS

Tupaia belangeri was not studied using FANTOM5 data.

Lab

retro_tbel_4240 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.

---

Parental genes homology:

Parental genes homology involve 2 parental genes, and 3 retrocopies.

Species	Parental gene accession	Retrocopies number
Tupaia belangeri	ENSTBEG00000011873	2 retrocopies	retro_tbel_4240 , retro_tbel_4726,
Tupaia belangeri	ENSTBEG00000014942	1 retrocopy	retro_tbel_2999,