RetrogeneDB ID: retro_nleu_2393

Retrocopy location

• Organism: Gibbon (Nomascus leucogenys)
• Coordinates: GL397350.1:3353410..3354144(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: ACTG1
• Ensembl ID: ENSNLEG00000013385
• Aliases: None
• Description: None

Sequence

>retro_nleu_2393
GACAATGCCCCCCAGGGTATCTTGCCTTCCATCACGGGATGCCCACGGAACCAGTACATGACAGCAGGCATGGGTCAGAA
GGACTCCTATGTGGGTGACAAGGCCCAGAGCAAGAGAGGCATCCTGATCCTGAAATACCACATCCAGCACAGCATCATCA
CCAACTAGGACGACATGGAGATCTGGAACCACACCTTCTACAACAAGCTGCACACGGCTCCTGAGGAACATCCCATGCTG
CTGACTGAGGCTCTTCTGAACCCCAAGGCCAACTGTGAGAAGATGACCCAGATCATGTTTGAGACCTTCAACACCCCCAC
CATATATGTGCCATCCATGCTGTGCTGTTCCTGTATGCCTCTGGTTGTACCACTGGCATTGTGATGGACTCCAGTGATGG
GGTCACTCACACTACCCAGCTACGAGGGGTACACCCTCCCCAGTGCCAACCTATGTCTGGACCTGGCTGGCTAGGACCTG
ACCGACTACCTCACAAAGATCCTTACTGAGCGTGGCTACAGCTTCACCACCACGGCCCAGCAGGAAATCATGTATGCCAT
CAAGAAGAAGCTGTGCTACATTGCCCTGGACTTCAAGTAGGAGATGGCCACCATGGCCTCCAGCTTCTCCCTGGAGAAGA
GCTACAAGCTGCTCCAGAGCCAGGTCATCACCATCTGCAACGAGTAGTTCCACTGCCCTGGCCTCTCCTCCAGCCTTCCT
TCCTGGGCATGGAA

Alignment

ORF - retro_nleu_2393 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 72.11 %
• Parental protein coverage: 65.87 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  DDAPRAVFPSIVGRPRHQGVMVGMGQKDSYVGDEAQSKRGILTLKYPIEHGIVTNWDDMEKIWHHTFYNE
          D.AP....PSI.G.PR.Q....GMGQKDSYVGD.AQSKRGIL.LKY.I.H.I.TN.DDME.IW.HTFYN.
Retrocopy DNAPQGILPSITGCPRNQYMTAGMGQKDSYVGDKAQSKRGILILKYHIQHSIITN*DDME-IWNHTFYNK

Parental  LRVAPEEHPVLLTEAPLNPKANREKMTQIMFETFNTPAMYV-AIQAVLSLYASGRTTGIVMDSGDGVTHT
          L..APEEHP.LLTEA.LNPKAN.EKMTQIMFETFNTP..YV.AI.AVL.LYASG.TTGIVMDS.DGVTHT
Retrocopy LHTAPEEHPMLLTEALLNPKANCEKMTQIMFETFNTPTIYV<AIHAVLFLYASGCTTGIVMDSSDGVTHT

Parental  V-PIYEGYALP-HAILRLDLAGRDLTDYLMKILTERGYSFTTTAEREIVRDIKEKLCYVALDFEQEMATA
          ..P...G...P..A.L.LDLAG.DLTDYL.KILTERGYSFTTTA..EI...IK.KLCY.ALDF..EMAT.
Retrocopy T<PATRGTPSP<SANLCLDLAG*DLTDYLTKILTERGYSFTTTAQQEIMYAIKKKLCYIALDFK*EMATM

Parental  ASSSSLEKSYELPDGQVITIGNERFRCPE-ALFQPSFLGME
          ASS.SLEKSY.L...QVITI.NE.F.CP...L.QPSFLGME
Retrocopy ASSFSLEKSYKLLQSQVITICNE*FHCPG<PLLQPSFLGME

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_2393 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 19 parental genes, and 102 retrocopies.

Species	Parental gene accession	Retrocopies number
Anolis carolinensis	ENSACAG00000015238	3 retrocopies	retro_acar_176, retro_acar_199, retro_acar_7,
Bos taurus	ENSBTAG00000006189	2 retrocopies	retro_btau_286, retro_btau_903,
Callithrix jacchus	ENSCJAG00000002885	3 retrocopies	retro_cjac_139, retro_cjac_336, retro_cjac_377,
Gallus gallus	ENSGALG00000028749	1 retrocopy	retro_ggal_6,
Loxodonta africana	ENSLAFG00000009167	1 retrocopy	retro_lafr_116,
Macropus eugenii	ENSMEUG00000016247	57 retrocopies	retro_meug_1006, retro_meug_1010, retro_meug_1018, retro_meug_1042, retro_meug_105, retro_meug_1085, retro_meug_1147, retro_meug_1186, retro_meug_1200, retro_meug_1230, retro_meug_1237, retro_meug_1380, retro_meug_1414, retro_meug_1437, retro_meug_1529, retro_meug_1534, retro_meug_1557, retro_meug_1588, retro_meug_1613, retro_meug_1624, retro_meug_1654, retro_meug_1656, retro_meug_1664, retro_meug_1669, retro_meug_1708, retro_meug_1716, retro_meug_1723, retro_meug_1753, retro_meug_1763, retro_meug_18, retro_meug_1935, retro_meug_1969, retro_meug_197, retro_meug_1982, retro_meug_1991, retro_meug_2100, retro_meug_2176, retro_meug_218, retro_meug_270, retro_meug_333, retro_meug_370, retro_meug_379, retro_meug_468, retro_meug_506, retro_meug_556, retro_meug_574, retro_meug_581, retro_meug_61, retro_meug_735, retro_meug_790, retro_meug_833, retro_meug_90, retro_meug_900, retro_meug_915, retro_meug_924, retro_meug_925, retro_meug_959,
Microcebus murinus	ENSMICG00000014863	3 retrocopies	retro_mmur_23, retro_mmur_352, retro_mmur_6,
Nomascus leucogenys	ENSNLEG00000012233	1 retrocopy	retro_nleu_2313,
Nomascus leucogenys	ENSNLEG00000013385	15 retrocopies	retro_nleu_1008, retro_nleu_1058, retro_nleu_1059, retro_nleu_1150, retro_nleu_1347, retro_nleu_1474, retro_nleu_1729, retro_nleu_2193, retro_nleu_2393 , retro_nleu_2574, retro_nleu_2669, retro_nleu_3032, retro_nleu_344, retro_nleu_813, retro_nleu_974,
Nomascus leucogenys	ENSNLEG00000014347	1 retrocopy	retro_nleu_1585,
Nomascus leucogenys	ENSNLEG00000015157	1 retrocopy	retro_nleu_2751,
Nomascus leucogenys	ENSNLEG00000015506	3 retrocopies	retro_nleu_1525, retro_nleu_1536, retro_nleu_1930,
Oryctolagus cuniculus	ENSOCUG00000005867	1 retrocopy	retro_ocun_720,
Otolemur garnettii	ENSOGAG00000008040	3 retrocopies	retro_ogar_148, retro_ogar_1808, retro_ogar_2430,
Petromyzon marinus	ENSPMAG00000004161	1 retrocopy	retro_pmar_4,
Pelodiscus sinensis	ENSPSIG00000002102	2 retrocopies	retro_psin_25, retro_psin_4,
Rattus norvegicus	ENSRNOG00000036701	1 retrocopy	retro_rnor_715,
Ictidomys tridecemlineatus	ENSSTOG00000006868	2 retrocopies	retro_itri_1675, retro_itri_531,
Xenopus tropicalis	ENSXETG00000025116	1 retrocopy	retro_xtro_6,