RetrogeneDB ID: retro_nleu_127

Retrocopy location

• Organism: Gibbon (Nomascus leucogenys)
• Coordinates: ADFV01134967.1:77574..79203(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSNLEG00000000214
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: ATL3
• Ensembl ID: ENSNLEG00000004565
• Aliases: None
• Description: None

Sequence

>retro_nleu_127
ATGTTGTCCCCTCAGCGAGTGGCAGCAGCTGCCTCAAGAGGAGCAGGTGATGCCATGGAGAGCAGCAAGCCTGGTCCAGT
GCAGGTTGTTTTGGTTCAGAAAGATCAACATTCCTTTGAGTTAGATGAGAAAGCCTTGGCCAGCATCCTCTTGCAGGACC
ACATCCGAGATCTTGATGTGGTGGTGGTTTCAGTGACTGGTGCCTTCCGAAAGGGCAAGTCCTTCATTCTGGATTTTATG
CTACGATACTTATATTCTCAGAAGGAAAGTGGCCATTCAAATTGGTTGGGTGACCCAGAAGAACCGTTAACAGGATTTTC
ATGGAGGGGGGATCTGATCCAGAAACCACTGGGATTCAGATCTGGAGTGAAGTTTTCACTGTGGAGAAGCCAGGTGGGAA
GAAGTTTGCAGTTGTTTTGATGGATACCCGGGGGGGCATTTGATAGCCAGTCAACTGTGAAAGACTGTGCTACCATCTTT
GCTCTAAGCACTATGACTAGTTCTGTTCAGATTTATAATTTATCCCAGAACATTCAAGAAGATGATCTTCAACAGCTGCA
GCTCTTCACAGAATACGGTCGTCTGGCAATGGATGAAATTTTCCAAAAGCCTTTCCAGACACTGATGTTTTTGGTTAGAG
ACTGGAGTTTCCCTTATGAATATAGCTATGGACTCCAAGGAGGAATGGCATTTTTTGGATAAGCGTTTACAGGTGAAGGA
ACATCAACATGAAGAAATTCAGAATGTTCGAAATCACATTCACTCATGTTTCTCCGATGTCACCCGCTTTCTCTTACCAC
ATCCAGGACTCCAGGTGGCCACAAGCCCTGACTTTGAGGGGAAATTAAAAGATATTGCTGGTGAATTCAAAGAGCAGTTA
CAGGCACTGATACTGTATGTATTAAACCCATCTAAGTTAATGGAAAAGGAGATCAATGGCTCAAAGGTCGCCTGTCGGGG
ACTACTGGAGTTTTTTAAGGCATATATTAAAATTTATCAAGGAGAAGATCTGCCTCACCCCAAGTCCATGCTTCAGGCCA
CTGCTGAAGCCAACAATTTAGCAGGTGTAGCCTCTGCCAAGGACATTTATTATAAGAACATGAAGGAAGTTTGTGGGGGA
GAGAAACCTTATTTCTCTCCAGACATTCTAGAGGAGAAGCACTGTGAATTCAAACGACTTGCTCTGGACCATTGTAAGAA
GACCAACAAGATGGGTGGGAAGGATTTCAGCTTTCGTTACCAGCAGGAGCTGGAAGAGGAAATCAAGGAATTAAATTATA
TGAGAACTTCTGCAAGCACAATGGTAGCAAGAACGTCTTCAGCACCTTCCGAACCCCTGCAGTGCTGTTCACGGGCATTG
TACCTTTGTACGTAGCCTCAGGCCTCACTGGCTTCATAAGTCTTGAGGTTGTAGCCAAGTTGTTCAACTGTATGGTTGGA
CTACTGTTAATAGCGCTCCTCACCTGGGGCTACATCAGGTATTCTGGTCAATATCGTGAGCTGGGTGGAGCTATTGATTT
TGGTGCTGCATATGTGTTGGAGCAGGCTTCTTCTTGTATCGGTAATTCCACTCAGGCCACTATGAGGGATGCAGTTGTTG
GAAGACCACCCATAGATAAAAAAGCTCAA

Alignment

ORF - retro_nleu_127 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 92.69 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  MLSPQRVAAAASRGAGDAMESSKPGPVQVVLVQKDQHSFELDEKALASILLQDHIRDLDVVVVSVAGAFR
          MLSPQRVAAAASRGAGDAMESSKPGPVQVVLVQKDQHSFELDEKALASILLQDHIRDLDVVVVSV.GAFR
Retrocopy MLSPQRVAAAASRGAGDAMESSKPGPVQVVLVQKDQHSFELDEKALASILLQDHIRDLDVVVVSVTGAFR

Parental  KGKSFILDFMLRYLYSQKESGHSNWLGDPEEPLTGFSWRG-GSDPETTGIQIWSEVFTVEKPGGKKVAVV
          KGKSFILDFMLRYLYSQKESGHSNWLGDPEEPLTGFSWRG.GSDPETTGIQIWSEVFTVEKPGGKK.AVV
Retrocopy KGKSFILDFMLRYLYSQKESGHSNWLGDPEEPLTGFSWRG<GSDPETTGIQIWSEVFTVEKPGGKKFAVV

Parental  LMDTQG-AFDSQSTVKDCATIFALSTMTSSVQIYNLSQNIQEDDLQQLQLFTEYGRLAMDEIFQKPFQTL
          LMDT.G.AFDSQSTVKDCATIFALSTMTSSVQIYNLSQNIQEDDLQQLQLFTEYGRLAMDEIFQKPFQTL
Retrocopy LMDTRG>AFDSQSTVKDCATIFALSTMTSSVQIYNLSQNIQEDDLQQLQLFTEYGRLAMDEIFQKPFQTL

Parental  MFLVRDWSFPYEYSYGLQGGMAF-LDKRLQVKEHQHEEIQNVRNHIHSCFSDVTCFLLPHPGLQVATSPD
          MFLVRDWSFPYEYSYGLQGGMAF.LDKRLQVKEHQHEEIQNVRNHIHSCFSDVT.FLLPHPGLQVATSPD
Retrocopy MFLVRDWSFPYEYSYGLQGGMAF>LDKRLQVKEHQHEEIQNVRNHIHSCFSDVTRFLLPHPGLQVATSPD

Parental  FDGKLKDIAGEFKEQLQALIPYVLNPSKLMEKEINGSKVTCRGLLEYFKAYIKIYQGEDLPHPKSMLQAT
          F.GKLKDIAGEFKEQLQALI.YVLNPSKLMEKEINGSKV.CRGLLE.FKAYIKIYQGEDLPHPKSMLQAT
Retrocopy FEGKLKDIAGEFKEQLQALILYVLNPSKLMEKEINGSKVACRGLLEFFKAYIKIYQGEDLPHPKSMLQAT

Parental  AEANNLAAAASAKDIYYNNMEEVCGGEKPYLSPDILEEKHCEFKQLALDHFKKTKKMGGKD--FSFRYQQ
          AEANNLA..ASAKDIYY.NM.EVCGGEKPY.SPDILEEKHCEFK.LALDH.KKT.KMGGKD..F......
Retrocopy AEANNLAGVASAKDIYYKNMKEVCGGEKPYFSPDILEEKHCEFKRLALDHCKKTNKMGGKDFSFRYQQEL

Parental  ELE-EEIKELYENFCKHNGSKNVFSTFRTPAVLFTGIVALYIASGLTGFIGLEVVAQLFNCMVGLLLIAL
          E.E......LYENFCKHNGSKNVFSTFRTPAVLFTGIV.LY.ASGLTGFI.LEVVA.LFNCMVGLLLIAL
Retrocopy EEE<NQGIKLYENFCKHNGSKNVFSTFRTPAVLFTGIVPLYVASGLTGFISLEVVAKLFNCMVGLLLIAL

Parental  LTWGYIRYSGQYRELGGAIDFGAAYVLEQASSHIGNSTQATVRDAVVGRPPIDKKAQ
          LTWGYIRYSGQYRELGGAIDFGAAYVLEQASS.IGNSTQAT.RDAVVGRPPIDKKAQ
Retrocopy LTWGYIRYSGQYRELGGAIDFGAAYVLEQASSCIGNSTQATMRDAVVGRPPIDKKAQ

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_127 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 2 parental genes, and 2 retrocopies.

Species	Parental gene accession	Retrocopies number
Macropus eugenii	ENSMEUG00000016040	1 retrocopy	retro_meug_785,
Nomascus leucogenys	ENSNLEG00000004565	1 retrocopy	retro_nleu_127 ,