RetrogeneDB ID: retro_nleu_3100

Retrocopy location

• Organism: Gibbon (Nomascus leucogenys)
• Coordinates: GL398301.1:2736..3964(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: KRT6A
• Ensembl ID: ENSNLEG00000017748
• Aliases: None
• Description: None

Sequence

>retro_nleu_3100
CTTTTGGGGTAGCTTGGGTACGGCAAGGGTCTGGGTGGAGGCTGTGGTGGGGCCCATGATATGGGGGACATCACAGCCGT
CATGGTCAACCAGAGCCTACTGAGGCCCCTTAAGCTGGAGGTGGACCCCAACATTCAGGCCATGTGCACCCAGGAGAAGG
ACCAGTTCAAGACCCTCAACAACAAATTTGCCTCCTTCATCAACAAGTTACAGTTCCTGGTGCAATAGAACAAAATACTG
GAGACCAAGTAGAGCCTCCTAAAGCAGCAGAAGATGGCTCAGAGGAAGATGGACTGCATGATCAAGAGCTATATTAACCT
TCAGCAGCAGCTGGACACTATGGGCCAGGAGAAGCTGAAGCTGGAGGCGAAGTTTGGCAACACACAGGGACTGGTGGAAG
ACTTCAAGAACTAGTATGAGGATGAGATCAATATTGATACAGAAGAGAATGAATTTGTCCTCATCAAGAAGGATGTGGCT
GAAGCTTACATGAATGAGGTAAAGCAGGAGTCTTGCCTGGAAGGGCTGAATGATGAGATCAACTTCCTCAGGCGGCTGTA
TGAAGAGGAGATCACGGAGCTGCAGTCTCAGATCTCGGACACATCTGTGGTGCTGTCCGTGGACAACAGCCACTCCCTGG
ACATGGGCAGCATCATCGCTGAGGTTAAGGTCCAGCAAGAGGAGATCACCAACTGAAGCTGGGCTGGGGCTGAGAGCCTG
CACCAGGTCAAGTGTGAAGATCTGCAGGCACTGGCTGGGAAGCACTGGACGACTTGCGTCACACAAAGATGGAGATCTCA
GAGCTGACCTGGAACCTCAGCTGGCTCCAGGCTGAGATTGACAGCCTCAAAAACCAGTGGGCCTCCCTGCAGGCTGCCAT
CACGGATGCAGAGCAGCGTTGGGAGCTGGCCATTAAGGAAGCCAAGCTGTCTGTGCTGGAGGCCACCCAGCGGTGGGCAA
AGCAGGACATGGTGCGGCAGCTGTGCGAGTACCAGGAGCTGATGAATATCAAGCAGGCCTGGTCATCGAGATCGCCACCT
ACAGGAAGCTGCTGTAGGGCAAGGAGAGCTGGCTGGAATCTGGGATACAGAACATGAGTATCCACACGAAGACCACCGGT
GGCTACTCAGGTAGGCTGAGCTTGGCCTACGGGGCCCTCACAAGCCCTAGCCTCAGCTACAGTCTGGGCTCTAGATTTGG
CTCTGGCAGGGGCTCCAGCTCCTTCAGC

Alignment

ORF - retro_nleu_3100 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 51.18 %
• Parental protein coverage: 74.47 %
• Number of stop codons detected: 6
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  LAGGAGLAGGFGGPGFPVCPPGGIQEVTINQSLLTPLNLQIDPTIQRVRAEEREQIKTLNNKFASFIDKV
          L.G..G...G.GG........G.I..V..NQSLL.PL.L..DP.IQ.....E..Q.KTLNNKFASFI.K.
Retrocopy LLG*LGYGKGLGGGCGGAHDMGDITAVMVNQSLLRPLKLEVDPNIQAMCTQEKDQFKTLNNKFASFINKL

Parental  RFLEQQNKVLETKWTLLQEQGTKTVRQNLEPLFEQYINNLRRQLDSIVGERGRLDSELRGMQDLVEDFKN
          .FL.Q.NK.LETK..LL..Q..K............YIN.L..QLD....E...L.......Q.LVEDFKN
Retrocopy QFLVQ*NKILETK*SLLKQQ--KMAQRKMDCMIKSYIN-LQQQLDTMGQEKLKLEAKFGNTQGLVEDFKN

Parental  KYEDEINKRTAAENEFVTLKKDVDAAYMNKVELQAKADTLTDEINFLRALYDAELSQMQTHISDTSVVLS
          .YEDEIN..T..ENEFV..KKDV..AYMN.V........L.DEINFLR.LY..E....Q..ISDTSVVLS
Retrocopy *YEDEINIDTE-ENEFVLIKKDVAEAYMNEVKQESCLEGLNDEINFLRRLYEEEITELQSQISDTSVVLS

Parental  MDNNRNLDLDSIIAEVKAQYEEIAQRSRAEAESWYQTKYEELQVTAGRHG-DDLRNTKQEIAEINRMIQR
          .DN...LD..SIIAEVK.Q.EEI...S.A.AES..Q.K.E.LQ..AG.H..DDLR.TK.EI.E.......
Retrocopy VDNSHSLDMGSIIAEVKVQQEEITN*SWAGAESLHQVKCEDLQALAGKHW<DDLRHTKMEISELTWNLSW

Parental  LRSEIDHVKKQCANLQAAIADAEQRGEMALKDAKNKLEGLEDALQKAKQDLARLLKEYQELMNVKLA-LD
          L..EID..K.Q.A.LQAAI.DAEQR.E.A.K.A..KL..LE.....AKQD..R.L.EYQELMN.K.A.L.
Retrocopy LQAEIDSLKNQWASLQAAITDAEQRWELAIKEA--KLSVLEATQRWAKQDMVRQLCEYQELMNIKQA<LV

Parental  VEIATYRKLLEGEECRLNGEGVGQVNISVVQSTVSSGYGGASGIGSGLGLGGGSSYSYGSGLGVGGGFSS
          .EIATYRKLL.G.E..L.....G..N.S....T...GY.G......G.......SYS.GS..G.G.G.SS
Retrocopy IEIATYRKLL*GKESWLES---GIQNMSIHTKT-TGGYSGRLSLAYGALTSPSLSYSLGSRFGSGRGSSS

Parental  SS
          .S
Retrocopy FS

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_3100 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 9 parental genes, and 22 retrocopies.

Species	Parental gene accession	Retrocopies number
Microcebus murinus	ENSMICG00000002190	1 retrocopy	retro_mmur_1094,
Nomascus leucogenys	ENSNLEG00000017733	8 retrocopies	retro_nleu_1913, retro_nleu_225, retro_nleu_2285, retro_nleu_2421, retro_nleu_2485, retro_nleu_2727, retro_nleu_2787, retro_nleu_672,
Nomascus leucogenys	ENSNLEG00000017740	1 retrocopy	retro_nleu_1808,
Nomascus leucogenys	ENSNLEG00000017746	5 retrocopies	retro_nleu_2270, retro_nleu_2596, retro_nleu_354, retro_nleu_457, retro_nleu_852,
Nomascus leucogenys	ENSNLEG00000017748	2 retrocopies	retro_nleu_2823, retro_nleu_3100 ,
Nomascus leucogenys	ENSNLEG00000017753	1 retrocopy	retro_nleu_1726,
Nomascus leucogenys	ENSNLEG00000017758	2 retrocopies	retro_nleu_593, retro_nleu_726,
Nomascus leucogenys	ENSNLEG00000026579	1 retrocopy	retro_nleu_311,
Tupaia belangeri	ENSTBEG00000000416	1 retrocopy	retro_tbel_1535,