RetrogeneDB ID: retro_nleu_2288

Retrocopy location

• Organism: Gibbon (Nomascus leucogenys)
• Coordinates: GL397341.1:7844257..7845324(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: NAB1
• Ensembl ID: ENSNLEG00000006665
• Aliases: None
• Description: NGFI-A binding protein 1 (EGR1 binding protein 1) [Source:HGNC Symbol;Acc:7626]

Sequence

>retro_nleu_2288
GCCACCACCTGTGTGCAGAGCTTGGGACAGGGAAAGTCAGATGTGGTCGGGGACCTAGCACTGCAGAGTGCTGGGGAGTC
CAGACTCTGGCAAGGCCACCATGCCACCAAGAGCGAGCACAGCCTCTCCCCAGCAGACCTGGGCTCCCAAACGTCCCCAA
AGGAGAGCAGCGAGGCACTGGATGCTGCTGCTGTGCGTTCTGTGGCAGAGTGTGTGGAGCGGATGGCCCCCGCACTGCCG
AAAAGTGACTTGAACGAAGTGAAAGAGCTGCTAAAAACCAACAAGAAGTTGGCCAAAATGATTGGTCACATCTTCGAGAT
GAACGATAATGATCCACACAAAGAGGAGGAAATGCGGAAACACCGTGAATATGTGGCAGATTTGACTCAAAGAGGAAGGA
TGGAAAACATCTCATGCTTCATGAGCTCACTGTTAATGAAGCGGCTGCTCAACTCTGTGTGGAGAATAATGCTCTGCTGA
CAAGAAGAGATGAGCATTTTGCCTTGGCTAGGCAGATTTCTCGCGAAGTCACCTATAAATATACTTACAGAACCACCAAG
TCAAAATGTGAAGAAAGAGATGAATTATCCCCGTAGAGGATTAAAGTGGAGGATGGGTTTCCAGATTTCCAGGATTCTGT
GCAAACGCTCTGCCAGCTGGCTAGAGCTAAGAGTGAAGAACTCGCGGCTCTTAGTTCACAGCAGCCTGAAAAGGTGATGG
CAAAGCAGATGGAGTCCCTTTGCAACCAAGTTGGCTATGAGAGACTGCAGCATGCCGAGAGGAGGCTGTCTGCAGGGCTT
TACAGGCAGAGCTCAGAAGAGCACAGTCCTAAAGGCTTGACTTCCGATAACTCAGACGGACAAGGAGAAAGAGCTTTGAA
TCTCCGAATGCCTAATTTACAGAACAGACAACCCCATCATTTTGTGGTGGATGGGGAGCTGAGCAGACTTTATCCCAGTG
AGGCAAAGTCCCACTCATCAGAGAGCCTTGGGAGTTTAAAAGACCACCCTCACTCAGCTTTTACCTTAGAAAAGAAAATC
ATCAAAACAGACCCTGAAGATTCAAGG

Alignment

ORF - retro_nleu_2288 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 91.04 %
• Parental protein coverage: 70.44 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  ATTCVQSLGQGKSDVVGSLALQSVGESRLWQGHHATESEHSLSPADLGSPASPKESSEALDAAAALSVAE
          ATTCVQSLGQGKSDVVG.LALQS.GESRLWQGHHAT.SEHSLSPADLGS..SPKESSEALDAAA..SVAE
Retrocopy ATTCVQSLGQGKSDVVGDLALQSAGESRLWQGHHATKSEHSLSPADLGSQTSPKESSEALDAAAVRSVAE

Parental  CVERMAPTLPKSDLNEVKELLKTNKKLAKMIGHIFEMNDDDPHKEEEIRKYSA-IYGRFDSKRKDGKHLT
          CVERMAP.LPKSDLNEVKELLKTNKKLAKMIGHIFEMND.DPHKEEE.RK....I.GRFDSKRKDGKHL.
Retrocopy CVERMAPALPKSDLNEVKELLKTNKKLAKMIGHIFEMNDNDPHKEEEMRKHRE<ICGRFDSKRKDGKHLM

Parental  LHELTVNEAAAQLCVKDNALLTRRDELFALARQISREVTYKYTYRTTKSKCGERDELSPKRIKVEDGFPD
          LHELTVNEAAAQLCV..NALLTRRDE.FALARQISREVTYKYTYRTTKSKC.ERDELSP.RIKVEDGFPD
Retrocopy LHELTVNEAAAQLCVENNALLTRRDEHFALARQISREVTYKYTYRTTKSKCEERDELSP*RIKVEDGFPD

Parental  FQDSVQTLFQQARAKSEELAALSSQ-PEKVMAKQMEFLCNQAGYERLQHAERRLSAGLYRQSSEEHSPNG
          FQDSVQTL.Q.ARAKSEELAALSSQ.PEKVMAKQME.LCNQ.GYERLQHAERRLSAGLYRQSSEEHSP.G
Retrocopy FQDSVQTLCQLARAKSEELAALSSQQPEKVMAKQMESLCNQVGYERLQHAERRLSAGLYRQSSEEHSPKG

Parental  LTSDNSDGQGERPLNLRMPNLQNRQPHHFVVDGELSRLYPSEAKSHSSESLGILKDYPHSAFTLEKKVIK
          LTSDNSDGQGER.LNLRMPNLQNRQPHHFVVDGELSRLYPSEAKSHSSESLG.LKD.PHSAFTLEKK.IK
Retrocopy LTSDNSDGQGERALNLRMPNLQNRQPHHFVVDGELSRLYPSEAKSHSSESLGSLKDHPHSAFTLEKKIIK

Parental  TEPEDSR
          T.PEDSR
Retrocopy TDPEDSR

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_2288 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 9 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000010241	1 retrocopy	retro_chof_2490,
Callithrix jacchus	ENSCJAG00000005748	1 retrocopy	retro_cjac_4224,
Gorilla gorilla	ENSGGOG00000013842	1 retrocopy	retro_ggor_3068,
Microcebus murinus	ENSMICG00000007306	2 retrocopies	retro_mmur_1155, retro_mmur_1211,
Nomascus leucogenys	ENSNLEG00000006665	1 retrocopy	retro_nleu_2288 ,
Pongo abelii	ENSPPYG00000013025	1 retrocopy	retro_pabe_3822,
Ictidomys tridecemlineatus	ENSSTOG00000000098	1 retrocopy	retro_itri_1621,
Tupaia belangeri	ENSTBEG00000011954	1 retrocopy	retro_tbel_3626,