RetrogeneDB ID: retro_tbel_2357

Retrocopy location

• Organism: Treeshrew (Tupaia belangeri)
• Coordinates: scaffold_109519:49217..49790(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSTBEG00000012322
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: SEC11C
• Ensembl ID: ENSTBEG00000014804
• Aliases: None
• Description: SEC11 homolog C (S. cerevisiae) [Source:HGNC Symbol;Acc:23400]

Sequence

>retro_tbel_2357
ATGGTGCGTGCAGGCAGCGTGGGGACACATCTCCCCGCGTCCGGTTTAGACATCTTCGGGGACCTGAGAAAGATGAACAA
GCGCCAGCTCTATTATCAGGTCCTCAACTTCGCCATGATCGTGTCTTCTGCACTCATGATATGGAAAGGCTTGATCGTGT
CACGGGCAGCGAAAGCCCGATCGTGGTGGTGTTGAGTGGCAGTATGGAGCCAGCCTTTCACGGGCGAGATCTTCTGTTCC
TCACAAATTTCCGGGAAGACCCCATTAGAGCTGGTGAAATAGTTGTTTTTAAAGTTGAAGGACGAGACATTCCAATAGTT
CACAGAGTAATCAAAATTCATGAAAAGGATAATGGAGACATCCAATTTCTGACTAAAGGGGATAATAATGAAGTCGATGA
TAGAGGCTTGTACAAAGGCCAGAACTGGCTGGAAGGGAAGGACGTAGTGGGACGAGCAAGAGGGTTTTTACCGTATGTTG
GTATGGTCACCATAATAATAAACGACTACCCGAAAATCCAAGTATGCTCTTTTGGCTGTGATGGGTGCGTATGTGTTACT
AAAACGTGAATCC

Alignment

ORF - retro_tbel_2357 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 93.81 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  MVRAGSVGTHLPASGLDIFGDLRKMNKRQLY-QVLNFAMIVSSALMIWKGLIV-LTGSESPIVVVLSGSM
          MVRAGSVGTHLPASGLDIFGDLRKMNKRQLY.QVLNFAMIVSSALMIWKGLIV..TGSESPIVVVLSGSM
Retrocopy MVRAGSVGTHLPASGLDIFGDLRKMNKRQLYYQVLNFAMIVSSALMIWKGLIV<VTGSESPIVVVLSGSM

Parental  EPAFHRGDLLFLTNFREDPIRAGEIVVFKVEGRDIPIVHRVIKVHEKDNGDIKFLTKGDNNEVDDRGLYK
          EPAFH..DLLFLTNFREDPIRAGEIVVFKVEGRDIPIVHRVIK.HEKDNGDI.FLTKGDNNEVDDRGLYK
Retrocopy EPAFHGRDLLFLTNFREDPIRAGEIVVFKVEGRDIPIVHRVIKIHEKDNGDIQFLTKGDNNEVDDRGLYK

Parental  EGQNWLEKKDVVGRARGFLPYVGMVTIIMNDYPKF-KYALLAVMGAYVLLKRES
          .GQNWLE.KDVVGRARGFLPYVGMVTII.NDYPK..KYALLAVMGAYVLLKRES
Retrocopy -GQNWLEGKDVVGRARGFLPYVGMVTIIINDYPKI>KYALLAVMGAYVLLKRES

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_2357 retrocopy.

TSS

Tupaia belangeri was not studied using FANTOM5 data.

Lab

retro_tbel_2357 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 12 parental genes, and 24 retrocopies.

Species	Parental gene accession	Retrocopies number
Equus caballus	ENSECAG00000017024	3 retrocopies	retro_ecab_1009, retro_ecab_455, retro_ecab_989,
Echinops telfairi	ENSETEG00000005115	2 retrocopies	retro_etel_1081, retro_etel_1139,
Felis catus	ENSFCAG00000006501	1 retrocopy	retro_fcat_1815,
Microcebus murinus	ENSMICG00000016052	1 retrocopy	retro_mmur_271,
Monodelphis domestica	ENSMODG00000020427	2 retrocopies	retro_mdom_1517, retro_mdom_377,
Oryctolagus cuniculus	ENSOCUG00000009204	2 retrocopies	retro_ocun_738, retro_ocun_895,
Otolemur garnettii	ENSOGAG00000002570	1 retrocopy	retro_ogar_400,
Pteropus vampyrus	ENSPVAG00000002950	2 retrocopies	retro_pvam_620, retro_pvam_869,
Sus scrofa	ENSSSCG00000004912	1 retrocopy	retro_sscr_775,
Tupaia belangeri	ENSTBEG00000012320	3 retrocopies	retro_tbel_1139, retro_tbel_2280, retro_tbel_745,
Tupaia belangeri	ENSTBEG00000014804	1 retrocopy	retro_tbel_2357 ,
Tursiops truncatus	ENSTTRG00000007676	5 retrocopies	retro_ttru_1278, retro_ttru_1508, retro_ttru_1780, retro_ttru_1916, retro_ttru_490,