RetrogeneDB ID: retro_nleu_1342

Retrocopy location

• Organism: Gibbon (Nomascus leucogenys)
• Coordinates: GL397289.1:21366736..21367638(-)
• Located in intron of: ENSNLEG00000005301

Retrocopy information

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

Parental gene information

• Parental gene symbol: CNN3
• Ensembl ID: ENSNLEG00000011207
• Aliases: None
• Description: None

Sequence

>retro_nleu_1342
TTCAACAAGGGCCCCTCATACTGGCTCTCTGCCGAGGTCAAGAACCAGATCCTGTCCAAATATGACCCCCAGAAGGAGGC
AGAGCTCCACAGCTGGATCGAGGGACTCACCAGTCTCTCCATCGGCCCTGACTTCCAGAAGGGCCTGAAGGACAGAATTA
TCTTACACACACTCATGAACGAGCTGCATCCAGGCTCAGTCCCCAAGATCAACCACTCCATGCAGAAACTGGCACCAGCT
AGAAAACCTCTCCAACTTCATCAAGGCCATAGTCAGCTATGGCATGAACCCCATGGACCTGTTTGATGCCAATAACCTGT
TTGAGAGTGGGAACATGACGCAGGTGCAGGTGTCTCTTCTTGCCCTGGCGGGGAAGGCCAAGACTAAGGGGCTGCAGAGC
GGGGTGGATATCGGCATCAGGTACTCAAAGAAGCAGGAGCGGAACTTCGACTACAACACCACGAAGGCTGGCCAGTGCGT
CATTGGGCTGCAGATGGGCACCAACAAATGTGCTAGCCAGTCGGGTATCATCATGTACGGCACAAGGCGCATCTCTACAG
CCCCAAGAACCACATCCTGCCGCCGTGGACCACTCGACCATCAGCCTCCAGATGGGTACAAACAAGTGCGCCAGCCACGT
GGGCATGACGGCTCCCTGGACCCAGCGGCACATCTATGACACCAAGCTGGGCACCAACAAGTGTGATAACTCCTCCATGT
CCCTGCAGATGGGCTACATGCAGGGTGCTAACCAGAGCAGCCAGGTCTTCAGCCTGGGCCGGCAGATATACAATTCCAAG
TACTGCCCACAAGGCCCAGCGGCCAACAGGGCTCCCTCGGGCACCAACGACTGCCCAGGCCCAGGGAAGGCCCCTGAATA
TCCCCCTTACTACCAGGAGGAG

Alignment

ORF - retro_nleu_1342 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 57.65 %
• Parental protein coverage: 92.4 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  FNKGPSYGLSAEVKNKIASKYDHQAEEDLRNWIEEVTGMSIGTNFQLGLKDGIILCELINKLQPGSVKKV
          FNKGPSY.LSAEVKN.I.SKYD.Q.E..L..WIE..T..SIG..FQ.GLKD.IIL..L.N.L.PGSV.K.
Retrocopy FNKGPSYWLSAEVKNQILSKYDPQKEAELHSWIEGLTSLSIGPDFQKGLKDRIILHTLMNELHPGSVPKI

Parental  NESSL-NWPQLENIGNFIKAIQAYGMKPHDIFEANDLFENGNMTQVQTTLVALAGLAKTKGFHTTIDIGV
          N.S...NW.QLEN..NFIKAI..YGM.P.D.F.AN.LFE.GNMTQVQ..L.ALAG.AKTKG.....DIG.
Retrocopy NHSMQ>NWHQLENLSNFIKAIVSYGMNPMDLFDANNLFESGNMTQVQVSLLALAGKAKTKGLQSGVDIGI

Parental  KYAEKQTRRFDEGKLKAGQSVIGLQMGTNKCASQAGMTAYGTRR-HLYDPKMQTDKPF-DQTTISLQMGT
          .Y..KQ.R.FD....KAGQ.VIGLQMGTNKCASQ.G...YGTRR.HLY.PK.....P..D..TISLQMGT
Retrocopy RYSKKQERNFDYNTTKAGQCVIGLQMGTNKCASQSGIIMYGTRR<HLYSPKNHILPPW<DHSTISLQMGT

Parental  NKGASQAGMLAPGTRRDIYDQKLTLQPVDNSTISLQMGTNKVASQKGMSVYGLGRQVYDPKYCAAPTEPV
          NK.AS..GM.AP.T.R.IYD.KL.....DNS..SLQMG....A.Q....V..LGRQ.Y..KYC..P..P.
Retrocopy NKCASHVGMTAPWTQRHIYDTKLGTNKCDNSSMSLQMGYMQGANQSS-QVFSLGRQIYNSKYC--PQGPA

Parental  IHNGSQGTGTNGSEISDSDYQAEYPDE
          ......GT...........Y...Y..E
Retrocopy ANRAPSGTNDCPGPGKAPEYPPYYQEE

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_1342 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 36 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000018128	3 retrocopies	retro_cjac_1331, retro_cjac_533, retro_cjac_861,
Equus caballus	ENSECAG00000020188	1 retrocopy	retro_ecab_655,
Echinops telfairi	ENSETEG00000010095	1 retrocopy	retro_etel_638,
Macropus eugenii	ENSMEUG00000002921	2 retrocopies	retro_meug_2020, retro_meug_42,
Monodelphis domestica	ENSMODG00000004326	1 retrocopy	retro_mdom_442,
Nomascus leucogenys	ENSNLEG00000001161	2 retrocopies	retro_nleu_1757, retro_nleu_2893,
Nomascus leucogenys	ENSNLEG00000011207	5 retrocopies	retro_nleu_122, retro_nleu_1342 , retro_nleu_2698, retro_nleu_480, retro_nleu_668,
Nomascus leucogenys	ENSNLEG00000013350	1 retrocopy	retro_nleu_575,
Pan troglodytes	ENSPTRG00000000979	15 retrocopies	retro_ptro_1061, retro_ptro_1149, retro_ptro_1247, retro_ptro_1447, retro_ptro_1505, retro_ptro_1554, retro_ptro_1871, retro_ptro_215, retro_ptro_2323, retro_ptro_2377, retro_ptro_2831, retro_ptro_2894, retro_ptro_3007, retro_ptro_483, retro_ptro_653,
Sarcophilus harrisii	ENSSHAG00000002670	1 retrocopy	retro_shar_567,
Tarsius syrichta	ENSTSYG00000010749	2 retrocopies	retro_tsyr_1458, retro_tsyr_1907,
Vicugna pacos	ENSVPAG00000004889	2 retrocopies	retro_vpac_190, retro_vpac_449,