RetrogeneDB ID: retro_nleu_673

Retrocopy location

• Organism: Gibbon (Nomascus leucogenys)
• Coordinates: GL397269.1:23916387..23917399(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSNLEG00000004822
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: HNRPDL
• Ensembl ID: ENSNLEG00000008636
• Aliases: None
• Description: None

Sequence

>retro_nleu_673
GATCTCTTCCACCGCCATTTTAAATTCAGCTCCATACAACACTCTGCCACCGCTGCTGCTGCACCCCGGACTGCGCGCCA
GCACCCCCCTGCTGACAGCTCCGCCACTATGGAGGATATGAACGAATACAGCAATATAGAGGAATTCGCAGAGGGATCCA
AGATCAACGCGAGCAAGGATCAGCAGGATGATGGTAAAATGTTTATTGGAGGCTTGAGCTGGGATACAAGCAAAAAAGAT
CTGAGAGGGTATGTGTCTCGATTTGGGAAAGTTGTAGACTGCACAATTAAAACAGATCCAGTCACTGGGAAATCAAGAAA
GTTTGGATTTCTGCTTTTCAAAGATGCTGCTGGTGTTGATAAGGTTTTGGAACTGAAAGAACACAAACTGGATGGCAAAT
TGATAGATCCCAAAAGGGCTAAAGCTTTAAAAGGGAAAGAACCCCCCAAAAAGGTTTTTATGGGTGGATTGAGCCCGGAT
ACTTCTGAAGAACAAATTAAAGAATATTTTGGAGCCTTTGGAGAGATTGAAAATATTGAACTTCCCATGGATACAAAAAC
AAATGAAAGAAGAGGATTTTGTTTTATCACATATACCAATGAAGAGCCAGTAAAAAGATTGTTAGAAAGCAGATACCATC
AAATTGGTTCTGCGAAGTGTGAAATCAAAGTTGCACAACCCAAAGAGGTATATACACAGCAACAGCAACAACAAAAAGGT
GGAAGAGGTACTGCAGCTGGTGGACAAGGTGGTACGAGGGGTCGTGGCCGAGGTCAGGGCCAAAACTGGAACCAAGGATT
TAATAGCTATTATGATCAAGGATATGGAAATTACAATAGTGCCTATGGTGGTGATCAAAACTATAGTGGCTATGGCGGAT
ATGATTATACTGTGTATAACTATGGGAACTATGGATATGGACAGGAATATGCAGACTACAGTGGCCAACAGAGCACTTTA
TGGCAAGGCATCTCGAGGGGGTGGCAATCACCAAAACAATTACCAGCCATAC

Alignment

ORF - retro_nleu_673 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 92.6 %
• Parental protein coverage: 80.24 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  DLFRRHFKSSSIQRSAAAAAATRTARQHPPADSSATMEDMNEYSNIEEFAEGSKINASKNQQDDGKMFIG
          DLF.RHFK.SSIQ.SA.AAAA.RTARQHPPADSSATMEDMNEYSNIEEFAEGSKINASK.QQDDGKMFIG
Retrocopy DLFHRHFKFSSIQHSATAAAAPRTARQHPPADSSATMEDMNEYSNIEEFAEGSKINASKDQQDDGKMFIG

Parental  GLSWDTSKKDLTEYLSRFGEVVDCTIKTDPVTGRSRGFGFVLFKDAASVDKVLELKEHKLDGKLIDPKRA
          GLSWDTSKKDL..Y.SRFG.VVDCTIKTDPVTG.SR.FGF.LFKDAA.VDKVLELKEHKLDGKLIDPKRA
Retrocopy GLSWDTSKKDLRGYVSRFGKVVDCTIKTDPVTGKSRKFGFLLFKDAAGVDKVLELKEHKLDGKLIDPKRA

Parental  KALKGKEPPKKVFVGGLSPDTSEEQIKEYFGAFGEIENIELPMDTKTNERRGFCFITYTDEEPVKKLLES
          KALKGKEPPKKVF.GGLSPDTSEEQIKEYFGAFGEIENIELPMDTKTNERRGFCFITYT.EEPVK.LLES
Retrocopy KALKGKEPPKKVFMGGLSPDTSEEQIKEYFGAFGEIENIELPMDTKTNERRGFCFITYTNEEPVKRLLES

Parental  RYHQIGSGKCEIKVAQPKEVYRQQQQQQKGGRGAAAGGRGGTRGRGRGQGQNWNQGFNNYYDQGYGNYNS
          RYHQIGS.KCEIKVAQPKEVY.QQQQQQKGGRG.AAGG.GGTRGRGRGQGQNWNQGFN.YYDQGYGNYNS
Retrocopy RYHQIGSAKCEIKVAQPKEVYTQQQQQQKGGRGTAAGGQGGTRGRGRGQGQNWNQGFNSYYDQGYGNYNS

Parental  AYGGDQNYSGYGGYDYTGYNYGNYGYGQGYADYSGQQST-YGKASRGGGNHQNNYQPY
          AYGGDQNYSGYGGYDYT.YNYGNYGYGQ.YADYSGQQST.YGKASRGGGNHQNNYQPY
Retrocopy AYGGDQNYSGYGGYDYTVYNYGNYGYGQEYADYSGQQST>YGKASRGGGNHQNNYQPY

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_673 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 12 parental genes, and 58 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000008940	1 retrocopy	retro_cfam_1086,
Choloepus hoffmanni	ENSCHOG00000000160	8 retrocopies	retro_chof_115, retro_chof_1470, retro_chof_2108, retro_chof_2370, retro_chof_533, retro_chof_59, retro_chof_741, retro_chof_890,
Choloepus hoffmanni	ENSCHOG00000003275	2 retrocopies	retro_chof_1578, retro_chof_18,
Dipodomys ordii	ENSDORG00000000968	1 retrocopy	retro_dord_145,
Loxodonta africana	ENSLAFG00000008612	1 retrocopy	retro_lafr_650,
Myotis lucifugus	ENSMLUG00000014452	2 retrocopies	retro_mluc_1140, retro_mluc_1761,
Mustela putorius furo	ENSMPUG00000014753	2 retrocopies	retro_mputfur_1359, retro_mputfur_600,
Nomascus leucogenys	ENSNLEG00000008636	1 retrocopy	retro_nleu_673 ,
Nomascus leucogenys	ENSNLEG00000015775	1 retrocopy	retro_nleu_1611,
Nomascus leucogenys	ENSNLEG00000017659	34 retrocopies	retro_nleu_1011, retro_nleu_1090, retro_nleu_1257, retro_nleu_130, retro_nleu_132, retro_nleu_1497, retro_nleu_1630, retro_nleu_1648, retro_nleu_166, retro_nleu_167, retro_nleu_1695, retro_nleu_1739, retro_nleu_1774, retro_nleu_1802, retro_nleu_1875, retro_nleu_190, retro_nleu_2040, retro_nleu_2222, retro_nleu_2304, retro_nleu_2324, retro_nleu_2378, retro_nleu_2690, retro_nleu_2742, retro_nleu_2852, retro_nleu_32, retro_nleu_366, retro_nleu_458, retro_nleu_587, retro_nleu_601, retro_nleu_645, retro_nleu_648, retro_nleu_708, retro_nleu_825, retro_nleu_987,
Otolemur garnettii	ENSOGAG00000002501	4 retrocopies	retro_ogar_2717, retro_ogar_2791, retro_ogar_437, retro_ogar_693,
Rattus norvegicus	ENSRNOG00000002270	1 retrocopy	retro_rnor_1365,