RetrogeneDB ID: retro_nleu_3102

Retrocopy location

• Organism: Gibbon (Nomascus leucogenys)
• Coordinates: GL398413.1:8402..8951(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSNLEG00000000411
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: SSR2
• Ensembl ID: ENSNLEG00000012304
• Aliases: None
• Description: None

Sequence

>retro_nleu_3102
ATGAGGCTGCTGTCATTTGTGGTGTTGGCTCTATTTGCTGTCACTTAAGCAGAGGAAGGAGCCAGGCTTTTGGTTTCCAA
ATCACTGCTGAACAGATACGTCGTGGAGGGACGAGACCTGAACTTGCAGTACAACATCTACAATGTCGGCTCAAGTGCTG
CATTAGACGTGGAACTATCTGATGATTCCTTCCCTCCAGAAGACTTTGGCATTGTGTCTGGAATGCTCAATGTCAAATGG
GACCGGATTGCCCCTGCTAGCAACGTCTCCCACACCATGGTCCTGCGCCCTCTCAAGGCTGGTTATTTCAACTTCACCTC
AGCAGCAATTACTTACCTGGCCCAGGAGGATGGGCCTGTTGTGATTGGCTCTAGCAGTGCACCTGGACAGGGAGGAATCC
TGGCTCAGCGGGAGTTTGACAAGCGATTCTTCCCTCATTTTCTGGACTGGGCAGCCTTTGGGGTCATGACCCTTCCCTCC
ATCGGCACCCCCCTGCTATTGTGGTACTCCAGCAAGAGGAAATATGACACTCCCAAAACGAAGAAGAAC

Alignment

ORF - retro_nleu_3102 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 94.54 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MRLLSFVVLALFAVTQAEEGARLLASKSLLNRYAVEGRDLTLQYNIYNVGSSAALDVELSDDSFPPEDFG
          MRLLSFVVLALFAVT.AEEGARLL.SKSLLNRY.VEGRDL.LQYNIYNVGSSAALDVELSDDSFPPEDFG
Retrocopy MRLLSFVVLALFAVT*AEEGARLLVSKSLLNRYVVEGRDLNLQYNIYNVGSSAALDVELSDDSFPPEDFG

Parental  IVSGMLNVKWDRIAPASNVSHTVVLRPLKAGYFNFTSATITYLAQEDGPVVIGSTSAPGQGGILAQREFD
          IVSGMLNVKWDRIAPASNVSHT.VLRPLKAGYFNFTSA.ITYLAQEDGPVVIGS.SAPGQGGILAQREFD
Retrocopy IVSGMLNVKWDRIAPASNVSHTMVLRPLKAGYFNFTSAAITYLAQEDGPVVIGSSSAPGQGGILAQREFD

Parental  RRFSPHFLDWAAFGVMTLPSIGIPLLLWYSSKRKYDTPKTKKN
          .RF.PHFLDWAAFGVMTLPSIG.PLLLWYSSKRKYDTPKTKKN
Retrocopy KRFFPHFLDWAAFGVMTLPSIGTPLLLWYSSKRKYDTPKTKKN

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_3102 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 4 parental genes, and 5 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000001212	2 retrocopies	retro_btau_1165, retro_btau_675,
Cavia porcellus	ENSCPOG00000023729	1 retrocopy	retro_cpor_478,
Nomascus leucogenys	ENSNLEG00000012304	1 retrocopy	retro_nleu_3102 ,
Ictidomys tridecemlineatus	ENSSTOG00000028971	1 retrocopy	retro_itri_1381,