RetrogeneDB ID: retro_nleu_2549

Retrocopy location

• Organism: Gibbon (Nomascus leucogenys)
• Coordinates: GL397370.1:682923..683949(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: BBS4
• Ensembl ID: ENSNLEG00000014060
• Aliases: None
• Description: None

Sequence

>retro_nleu_2549
ATATTTCGCCTGGAAGGAAATATCCAAGAATCCCTAGAACTCTTCCAGACATGTGCAGTTCTTAGCCCTCAGAGTGCAGA
TAACCTCAAGCAGGTGGCCAGATCTTTATTTCTTTTGGGAAAACATAAAGCTGCCATTGAAGTATATAATGAAGCAGCTA
AACTCAACCAGAAAGATTGGGCCATCTTGGCAGCAGGCAGCATGATGCAGACCTACGGGGACTTTGATGTTGCCCTCACC
AAATACAGAGTTGTGGCTTGTGCTGTTCCAGAAAGTCCTCCACTCTGGAATAACATTGGAATGTGTTTCTTTGGCAAGAA
GAAATATGTGGCGGCCATCAGCTGCCTGAAATGAGCCAACTACTTGGCACCCTTCGATTGGAAGATTCTGTATAATTTGG
GCCTTGTCCATTTGACCATGCAGCAGTATGCATCAGCTTTTCATTTTCTCACTGCAGCCATCAACTTCCAGCCAAAGATG
GGGGAGCTCTACATGCTCTTGGCAGTGGCTCTGACCAATCTGGAAGATATAGAGAATGCCAAGAGAGCCTACGCAAAAGC
AGTCCACCTGGATAAGTGTAACCCTTTAGTAAACCTGAACTATGCTGTGCTGCTGTACAACCAGGGCGAGAAGAAGAACA
CCCTGGCCCAATATCAGGAGATGGAGAAGAAAGTCAACCTACTCAAGGACAATAGCTCTCTGGAATTTGACTCTGAGATG
GTGGAGATGGCTCAGAATTTGGGAGCTGCTCTCCAGGTTGGGGAGGCACTGGTCTGGACTAAACCAGTTAAAGATCCCAA
ATCAAAGCACCAGACCACTTCAACCAGCAAACCTGCCAGTTTCCAGCAGCCTCTGGGCTCTAATCAAGCTCTAGGACAGG
CAATGTCTTCAGCAGCTGCATATAGGATGCTCCCCTCAAGTGCTGGAGGAACATCCCAGTTCACAAAGCCCCCATCTCTT
CCTCTGGAGCCAGAGCCTGTGGTGGAATCAATTCCAACTGAAATATCAGAACAAATAAGAGAGAAA

Alignment

ORF - retro_nleu_2549 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 81.92 %
• Parental protein coverage: 66.02 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  IHLLEGDLDKAIEIYKKAVEFSPENTQLLTTLGLLYLQLGIYQKAFEHLGNALTYDPTNYKAILAAGSIM
          I..LEG......E........SP.....L.........LG....A.E....A.........AILAAGS.M
Retrocopy IFRLEGNIQESLELFQTCAVLSPQSADNLKQVARSLFLLGKHKAAIEVYNEAAKLNQKDW-AILAAGSMM

Parental  QTHGDFDVALTKYRVVACAVPESPPLWNNIGMCFFGKKKYVAAISCLKRANYLAPFDWKILYNLGLVHLT
          QT.GDFDVALTKYRVVACAVPESPPLWNNIGMCFFGKKKYVAAISCLK.ANYLAPFDWKILYNLGLVHLT
Retrocopy QTYGDFDVALTKYRVVACAVPESPPLWNNIGMCFFGKKKYVAAISCLK*ANYLAPFDWKILYNLGLVHLT

Parental  MQQYASAFHFLSAAINFQPKMGELYMLLAVALTNLEDIENAKRAYAEAVHLDKCNPLVNLNYAVLLYNQG
          MQQYASAFHFL.AAINFQPKMGELYMLLAVALTNLEDIENAKRAYA.AVHLDKCNPLVNLNYAVLLYNQG
Retrocopy MQQYASAFHFLTAAINFQPKMGELYMLLAVALTNLEDIENAKRAYAKAVHLDKCNPLVNLNYAVLLYNQG

Parental  EKKNALAQYQEMEKKVNLLKDNSSLEFDSEMVEMAQKLGAALQVGEALVWTKPAKDPKSKHQTTSTSKPA
          EKKN.LAQYQEMEKKVNLLKDNSSLEFDSEMVEMAQ.LGAALQVGEALVWTKP.KDPKSKHQTTSTSKPA
Retrocopy EKKNTLAQYQEMEKKVNLLKDNSSLEFDSEMVEMAQNLGAALQVGEALVWTKPVKDPKSKHQTTSTSKPA

Parental  SFQQPLGSNQALGQAMSSAAAYRTLPSGAGGT-QFTKPPSLPLEPEPAVESIPTETSEQMREK
          SFQQPLGSNQALGQAMSSAAAYR.LPS.AGGT.QFTKPPSLPLEPEP.VESIPTE.SEQ.REK
Retrocopy SFQQPLGSNQALGQAMSSAAAYRMLPSSAGGTSQFTKPPSLPLEPEPVVESIPTEISEQIREK

Legend:

• *: Stop codon
• >: Forward frameshift by one nucleotide
• <: Reverse frameshift by one nucleotide

Expression

RNA-Seq

Nomascus leucogenys was not studied using RNA-Seq expression data.

ChIP-Seq

Nomascus leucogenys was not studied using ChIP-Seq data.

EST

Nomascus leucogenys was not studied using EST data.

TSS

Nomascus leucogenys was not studied using FANTOM5 data.

Lab

retro_nleu_2549 was not experimentally validated.

Homology

Retrocopy orthology:

Nomascus leucogenys 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 2 retrocopies.

Species	Parental gene accession	Retrocopies number
Nomascus leucogenys	ENSNLEG00000014060	1 retrocopy	retro_nleu_2549 ,
Pteropus vampyrus	ENSPVAG00000015883	1 retrocopy	retro_pvam_378,