RetrogeneDB ID: retro_nleu_1754

Retrocopy location

• Organism: Gibbon (Nomascus leucogenys)
• Coordinates: GL397307.1:15931539..15932608(+)
• Located in intron of: ENSNLEG00000013824

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSNLEG00000001476
• Aliases: None
• Description: None

Sequence

>retro_nleu_1754
TCTCAGGCTGACTGTGCTGTCCTGATTGTTGCTGCTGGTGCTGGTGAATTTGAAGCTGGTATCTCCAAGAATGGGCAGAC
CCGAGAGCATGCCCTTCTGGCTTACATACTGGGTGTGAAACAACTAATTGTTGGTGTTAACAAAATGGATTCCACTGAGC
CACCCTACAGCCAGAAGAGATATGAGGAAATCGTTAAGGAAGTCAGCACTTACATTAAGAAAATTGGCTACAACCCTGAC
ACAGTAGCATTTGTGCCAATTTCTGGTTGGAATGGTGACAACATGCTGGAGCCAAATGCTAACATGCCTTGGTTCAAGGG
ATGGAAAGTCACCCGTAAGGATGGCAATGCCAACGGAACCACGCTGCTTGAGGCTCTGGACTGCATCCTACCACCAGCTC
GTCCAACGGACAAGCCCTTGCGCCTGCCTCTCCAGGATGTCTACAAAATTGGTGGTATTGGTACCGTTCCTGTTGGCCGA
GTGGAGACTGGTGTTCTCAAATCTGGTATGGTGGTCACCTTTGCTCCAGTCAACGTTACAACAGAAGTAAAATCTGTCGA
AATGCACCATGAAGCTTTGAGGGAAGCTCTTCCTGGGGACAATGTGGGCTTCAATGTCAAGAATGTGTCTGTCAAGGATG
TTCGTCGTGGCAACGTTGCTGGTGACAGCAAAAATGACCCACCAATGGAAGGGGCTGGCGTCACTGCTCAGGTGATTATC
CTGAACCATCCAGGGCAAATAAGCGCTGGCTATGCCCCCTGTATTGGATTGCCACATGGCTCACATTGCATGCAAGTTTG
CTGAGCTGAAGGAAAAGACTGATCGCCGTTCTGGTAAAAAGCTGGAAGATGGCCCTAAATTCTTGAAGTCTGGTGATGCT
GCCATTATTGATACGGTTCCTGGCAAGCCTATGCGTGTTGGGAGCTTCTCAGACTATCCACTTTTGGGTCACTCTGCTGT
TCGTGATATGAGACAGACAGTTGCGGTGGGTGTCATCAAAGCAGTGGACAAGAAGGCTGCTGGAGCTGGCAAGGTCACCA
AGCCTGCCCAGAAAGCTCAGAAGGCTAAA

Alignment

ORF - retro_nleu_1754 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 94.4 %
• Parental protein coverage: 85.99 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  SQADCAVLIVAAGVGEFEAGISKNGQTREHALLAYTLGVKQLIVGVNKMDSTEPPYSQKRYEEIVKEVST
          SQADCAVLIVAAG.GEFEAGISKNGQTREHALLAY.LGVKQLIVGVNKMDSTEPPYSQKRYEEIVKEVST
Retrocopy SQADCAVLIVAAGAGEFEAGISKNGQTREHALLAYILGVKQLIVGVNKMDSTEPPYSQKRYEEIVKEVST

Parental  YIKKIGYNPDTVAFVPISGWNGDNMLEPSANMPWFKGWKVTRKDGNASGTTLLEALDCILPPTRPTDKPL
          YIKKIGYNPDTVAFVPISGWNGDNMLEP.ANMPWFKGWKVTRKDGNA.GTTLLEALDCILPP.RPTDKPL
Retrocopy YIKKIGYNPDTVAFVPISGWNGDNMLEPNANMPWFKGWKVTRKDGNANGTTLLEALDCILPPARPTDKPL

Parental  RLPLQDVYKIGGIGTVPVGRVETGVLKPGMVVTFAPVNVTTEVKSVEMHHEALSEALPGDNVGFNVKNVS
          RLPLQDVYKIGGIGTVPVGRVETGVLK.GMVVTFAPVNVTTEVKSVEMHHEAL.EALPGDNVGFNVKNVS
Retrocopy RLPLQDVYKIGGIGTVPVGRVETGVLKSGMVVTFAPVNVTTEVKSVEMHHEALREALPGDNVGFNVKNVS

Parental  VKDVRRGNVAGDSKNDPPMEAAGFTAQVIILNHPGQISAGYA-PVLDCHTAHIACKFAELKEKIDRRSGK
          VKDVRRGNVAGDSKNDPPME.AG.TAQVIILNHPGQISAGYA.PVLDCH.AHIACKFAELKEK.DRRSGK
Retrocopy VKDVRRGNVAGDSKNDPPMEGAGVTAQVIILNHPGQISAGYA>PVLDCHMAHIACKFAELKEKTDRRSGK

Parental  KLEDGPKFLKSGDAAIVDMVPGKPMCVESFSDYPPLGRFAVRDMRQTVAVGVIKAVDKKAAGAGKVTKSA
          KLEDGPKFLKSGDAAI.D.VPGKPM.V.SFSDYP.LG..AVRDMRQTVAVGVIKAVDKKAAGAGKVTK.A
Retrocopy KLEDGPKFLKSGDAAIIDTVPGKPMRVGSFSDYPLLGHSAVRDMRQTVAVGVIKAVDKKAAGAGKVTKPA

Parental  QKAQKAK
          QKAQKAK
Retrocopy QKAQKAK

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_1754 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 54 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000013249	1 retrocopy	retro_cfam_1007,
Cavia porcellus	ENSCPOG00000004067	15 retrocopies	retro_cpor_1150, retro_cpor_1162, retro_cpor_1191, retro_cpor_1256, retro_cpor_1393, retro_cpor_1492, retro_cpor_1499, retro_cpor_348, retro_cpor_381, retro_cpor_387, retro_cpor_413, retro_cpor_709, retro_cpor_891, retro_cpor_918, retro_cpor_959,
Dipodomys ordii	ENSDORG00000009629	1 retrocopy	retro_dord_509,
Equus caballus	ENSECAG00000022260	1 retrocopy	retro_ecab_802,
Erinaceus europaeus	ENSEEUG00000000342	3 retrocopies	retro_eeur_407, retro_eeur_492, retro_eeur_625,
Loxodonta africana	ENSLAFG00000028081	1 retrocopy	retro_lafr_651,
Monodelphis domestica	ENSMODG00000018533	4 retrocopies	retro_mdom_1053, retro_mdom_1146, retro_mdom_311, retro_mdom_792,
Mus musculus	ENSMUSG00000037742	15 retrocopies	retro_mmus_1349, retro_mmus_1518, retro_mmus_1667, retro_mmus_1783, retro_mmus_1816, retro_mmus_1849, retro_mmus_1850, retro_mmus_1864, retro_mmus_1909, retro_mmus_2363, retro_mmus_2583, retro_mmus_2902, retro_mmus_3249, retro_mmus_480, retro_mmus_483,
Nomascus leucogenys	ENSNLEG00000001476	6 retrocopies	retro_nleu_1492, retro_nleu_1584, retro_nleu_1754 , retro_nleu_1901, retro_nleu_235, retro_nleu_829,
Nomascus leucogenys	ENSNLEG00000010060	2 retrocopies	retro_nleu_11, retro_nleu_1489,
Ictidomys tridecemlineatus	ENSSTOG00000007687	4 retrocopies	retro_itri_1509, retro_itri_1740, retro_itri_1816, retro_itri_195,
Drosophila melanogaster	FBgn0000557	1 retrocopy	retro_dmel_9,