RetrogeneDB ID: retro_nleu_2775

Retrocopy location

• Organism: Gibbon (Nomascus leucogenys)
• Coordinates: GL397425.1:591735..592539(-)
• Located in intron of: ENSNLEG00000007613

Retrocopy information

• Ensembl ID: ENSNLEG00000007625
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: SF3A3
• Ensembl ID: ENSNLEG00000011720
• Aliases: None
• Description: None

Sequence

>retro_nleu_2775
TGGCCAAAAGAGACAAGCAGCGCTCTGACCCATGCTGGAGCCCATCCTGACCTCTCCGCATTCTCCTTCTGGGAGGAGTT
GGCCTCTCTGGGTTTGGACAGATTGAAATCTGCTCTCTTAGCTTTAGGCTTGAAATGTGGCGGACCGTAGAAGGGCAAGC
CCAGAGACTATTCAGCACCAAAGGAAAGTCCCTGGAGTCACTTGATAACTCTTTGTTTGCCAAAAATCCCAAATCAAAGG
GCACCAAGCGAGACACTGAGAGGAACAAAGACATTGCTTTTCTGGAAGCCCAGATCTATAAATACTCTGACTCTCGGGCA
ACAGCAACATCTCACTCATGAAAATGTACAGTGCACGCAAGCAAGGACAGGAGAAGAGCAAGAAGCGCAGATCAGTGACA
GTGAGAGTGAAGATGAAAAGAACGAGATCATTTACAACCCCAAAAACCTGCCACTTGGCTGGGATGGCAAACACATTTCC
TACTGGCTATATAAGCTTCATGGCCTAAATACCAACTATAACTGTGAGATCTGTGGAAACTACACCTACCAAGGGCCCAA
AGCCTTCCAGTGACACTTTGCTCAATAGCATCATGCTCATGGCATGAGGTGTTTGGGCATCCCAAACACTGCTCACTTTA
CTAATGTGACACAGATTGAAGATACTGTCTCCTTGTGGGCCAAACTCAAATTGCAGAAGGCTTCAGAATGATGGCAGCCT
GACACTGAGGAAGAATATGAAGACTCAAGTGGGAATGTTGTGAATAAGAAGACATATGAGGATCTGAAAAAACAAGGACT
GCTC

Alignment

ORF - retro_nleu_2775 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 77.82 %
• Parental protein coverage: 53.85 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  WPKPGSYALTHAGAHLDLSAFSSWEELASLGLDRLKSALLALGLKCGG-TLEERAQRLFSTKGKSLESLD
          WPK..S.ALTHAGAH.DLSAFS.WEELASLGLDRLKSALLALGLKCGG.T.E..AQRLFSTKGKSLESLD
Retrocopy WPKETSSALTHAGAHPDLSAFSFWEELASLGLDRLKSALLALGLKCGG<TVEGQAQRLFSTKGKSLESLD

Parental  TSLFAKN-PKSKGTKRDTERNKDIAFLEAQIYEYVEILGEQRHLTHENVQRKQARTGEEREEEEEEQISE
          .SLFAKN.P............K...F...........LG.Q.HLTHENVQ..QARTG....EE.E.QIS.
Retrocopy NSLFAKN>PNQRAPSETLRGTKTLLFWKPRSINTLT-LGQQQHLTHENVQCTQARTG----EEQEAQISD

Parental  SESEDEENEIIYNPKNLPLGWDGKPIPYWLYKLHGLNINYNCEICGNYTYRGPKAFQRHFAEWRHAHGMR
          SESEDE.NEIIYNPKNLPLGWDGK.I.YWLYKLHGLN.NYNCEICGNYTY.GPKAFQ.HFA...HAHGMR
Retrocopy SESEDEKNEIIYNPKNLPLGWDGKHISYWLYKLHGLNTNYNCEICGNYTYQGPKAFQ*HFAQ*HHAHGMR

Parental  CLGIPNTAHFANVTQIEDAVSLWAKLKLQKASERWQPDTEEEYEDSSGNVVNKKTYEDLKRQGLL
          CLGIPNTAHF.NVTQIED.VSLWAKLKLQKASE.WQPDTEEEYEDSSGNVVNKKTYEDLK.QGLL
Retrocopy CLGIPNTAHFTNVTQIEDTVSLWAKLKLQKASE*WQPDTEEEYEDSSGNVVNKKTYEDLKKQGLL

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_2775 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 11 parental genes, and 15 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000001262	1 retrocopy	retro_amel_485,
Canis familiaris	ENSCAFG00000003222	1 retrocopy	retro_cfam_176,
Callithrix jacchus	ENSCJAG00000002176	1 retrocopy	retro_cjac_4109,
Cavia porcellus	ENSCPOG00000008660	1 retrocopy	retro_cpor_658,
Homo sapiens	ENSG00000183431	2 retrocopies	retro_hsap_2441, retro_hsap_937,
Macropus eugenii	ENSMEUG00000002534	3 retrocopies	retro_meug_1135, retro_meug_1346, retro_meug_642,
Macaca mulatta	ENSMMUG00000023199	1 retrocopy	retro_mmul_631,
Monodelphis domestica	ENSMODG00000017729	1 retrocopy	retro_mdom_269,
Nomascus leucogenys	ENSNLEG00000011720	1 retrocopy	retro_nleu_2775 ,
Pan troglodytes	ENSPTRG00000000559	2 retrocopies	retro_ptro_1411, retro_ptro_649,
Sorex araneus	ENSSARG00000014204	1 retrocopy	retro_sara_407,