RetrogeneDB ID: retro_nleu_2409

Retrocopy location

• Organism: Gibbon (Nomascus leucogenys)
• Coordinates: GL397353.1:1642767..1643504(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: DNAJB14
• Ensembl ID: ENSNLEG00000013668
• Aliases: None
• Description: None

Sequence

>retro_nleu_2409
AGCTTGAAGTTTCATCCAGACAAAAACAATGCACCTGGAGCAACAGGTGCTTTTAAAAGGCTTGGAAATGCTTATGCTGT
TTTAAGTAATCCAGAAAGCGAAAACGGTATGACCTCACAGGCAATGAAGAGCAAGCATGTAACCACCAAAACAATGGCAG
ATTTAATTTCCATAGAGGTTGCGAAGCTGATATAACTCCAGAAGACTCGTTTAATATATTTTTGGGGGTGGATTTCCTTC
AGGTAGTGTACTTTCTTTTTCAAATGGATGAGCTGGTTATAGCCAACATCAGCATCGACATAGGGGACATGAAAGAGAAG
AGGAAAGAGGAGATAGAGGTTTTTCTGTGTTTATCCAGCTGATGCCCATAATCGTATTAATCCTCGTGTCATTATTAAGC
CAATTGATGGTCTCTAATCCTCCTTACTCCTTATATCCCAGATCTAGAACAGGGCAAACTACTAAAATGCAGACATAAAC
TTGGGTGTTGTTTATTACATCAAAAGGACTTTAAAAATGAATATAAAGGAATGTTATTACAAAAGGTAGAAAAGAGTGTG
GAAGAAGATTATGTGACTAATATTCGAAATAATCGCTGGAAAGAAAGACAACAAAAAACAGATATGCAATATGCAGCAAA
AGTATACTGTGATGATCGACTCTGAAGGAAGGCAGACGCCTTGAGCGTGGACAACTGTAAAGAATGAGAGAGGCTTACCA
GTCTTTATAAAGGAGGA

Alignment

ORF - retro_nleu_2409 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 89.68 %
• Parental protein coverage: 65.44 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  ALKFHPDKNHAPGATDAFKKIGNAYAVLSNPE-KRKQYDLTGNEEQACNHQNNGRFNFHRGCEADITPED
          .LKFHPDKN.APGAT.AFK..GNAYAVLSNPE.KRK.YDLTGNEEQACNHQNNGRFNFHRGCEADITPED
Retrocopy SLKFHPDKNNAPGATGAFKRLGNAYAVLSNPE<KRKRYDLTGNEEQACNHQNNGRFNFHRGCEADITPED

Parental  LFNIF-FGGGFPSGSVHSFSNGRAGYSQQHQHRHSGHEREEERGDGGFSVFIQLMPIIVLILVSLLSQLM
          .FNIF.FGGGFPSGSV.SFSNG.AGYSQ.HQHRH.GHEREEERGD.GFSVFIQLMPIIVLILVSLLSQLM
Retrocopy SFNIF<FGGGFPSGSVLSFSNG*AGYSQ-HQHRHRGHEREEERGDRGFSVFIQLMPIIVLILVSLLSQLM

Parental  VSNPPYSLYPRSGTGQTIKMQT-ENLGVVYYVN-KDFKNEYKGMLLQKVEKSVEEDYVTNIRNNCWKERQ
          VSNPPYSLYPRS.TGQT.KMQT..NLGVVYY...KDFKNEYKGMLLQKVEKSVEEDYVTNIRNN.WKERQ
Retrocopy VSNPPYSLYPRSRTGQTTKMQT<INLGVVYYIK<KDFKNEYKGMLLQKVEKSVEEDYVTNIRNNRWKERQ

Parental  QKTDMQYAAKVYRDDRLRRKADALSMDNCKELERLTSLYKGG
          QKTDMQYAAKVY.DDRL.RKADALS.DNCKE.ERLTSLYKGG
Retrocopy QKTDMQYAAKVYCDDRL*RKADALSVDNCKE*ERLTSLYKGG

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_2409 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.

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Parental genes homology:

Parental genes homology involve 8 parental genes, and 12 retrocopies.

Species	Parental gene accession	Retrocopies number
Anolis carolinensis	ENSACAG00000012468	1 retrocopy	retro_acar_144,
Homo sapiens	ENSG00000164031	1 retrocopy	retro_hsap_1583,
Monodelphis domestica	ENSMODG00000020687	2 retrocopies	retro_mdom_1398, retro_mdom_752,
Nomascus leucogenys	ENSNLEG00000013668	2 retrocopies	retro_nleu_1761, retro_nleu_2409 ,
Otolemur garnettii	ENSOGAG00000005340	1 retrocopy	retro_ogar_120,
Pongo abelii	ENSPPYG00000014956	3 retrocopies	retro_pabe_1304, retro_pabe_982, retro_pabe_983,
Pan troglodytes	ENSPTRG00000016311	1 retrocopy	retro_ptro_1066,
Ictidomys tridecemlineatus	ENSSTOG00000021338	1 retrocopy	retro_itri_1840,