RetrogeneDB ID: retro_amel_858

Retrocopy location

• Organism: Panda (Ailuropoda melanoleuca)
• Coordinates: GL192686.1:1231566..1232665(+)
• Located in intron of: ENSAMEG00000000288

Retrocopy information

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

Parental gene information

• Parental gene symbol: TOX4
• Ensembl ID: ENSAMEG00000006261
• Aliases: None
• Description: None

Sequence

>retro_amel_858
ATGACATCTCACTTGATGGGGCATAGTCAGTTGACCACCACTGATGAGTCAGAACAAAGTTCTCGACTTGGTTTGAGCTT
AGGGGGTGGCACCATACTTCCACCTGCCAGTCACTCAAGCATTGTCTTTCAACCACCCCTTCACCTATTAGTTCACTTCA
CAAGGATGGTGTTGAGGATTTCCGGAGGCAACTTCCCAGCCAGAAGACAGTTGTGTGGAAGCAGGAAAAAAGCAGAAGGC
CCCAAAGAAGAGAAAAAAAAAATCCTAATGAAGCTAAGAAGCCAGTTTCATCATCTGCTTTATTCTTTCGTGATACACGG
GCTGTCATCAAGGGACAGAATCCCAATGCGTCTTTTGAGGGGGTTTCAAAAATTGGGGCCTCCATGTAGGATAGTCTTGG
AAAGGAGCAAAAACAGGTGTATAAGAGGAAAACCGAAGCTGCCAAGAAAGCATCTGAAGGCTCTGGCAGAATATAAAGAC
ACTCAAGAGTGTCAGGCCACTGTGGAAACAATAGAATTGGACCCAGTGCCACCGTCACAGACTCCTTCTCCACCTCCTAT
GGCTACCGTTGACCCAGCGTCTCCCCCGCCAGCCTCAGCAGAGCCCCCTGCCCTGCCCCCTTCCATTGTTGTTAACTCCA
CTCTTTCCTTCTATGTGGCAAACCAGGCATCTTTTGGGGCTGGAGCTCAGCCCAGTGTCACCAAGTTGATTATTACCAGA
CAGATGTTGCCCTCTTCTGTGACTATGTCTCGAGGGATGGTTACCATTATCCCAGCCACAGTGGTGAACTCCCAGGGGAT
CCAACTAAGCCAAACCAGTACAGCCACTATCCAGCCCAGTCAACAAACCCAAATTGTCACTTGCTCAGTGTTGGAGAGGC
AGCATCCTCCACCCCAATGACAACCCCACCATTGCAACAGCTGCCTCAGCCCCCCACTCAGCAGCAAGTGACCATTCAGC
AGCAGCCTCCCTACTTCAGGTCATGCCACAGCCTCCACCTCAGAAAGTTCGAATCAATTTATGGCAACAGCCACCTGCTC
TACAGATCAAGATTGCACCTCCACCCACTCTGAAAATGCAGACCACCTTAGTCCCACCA

Alignment

ORF - retro_amel_858 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 65.7 %
• Parental protein coverage: 59.06 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  MTSGLMGHSQLTTIDQSELSSQLGLSLGGGTILPPA-QSPEDRLSTTPSPTSSLHEDGVEDFRRQLPSQK
          MTS.LMGHSQLTT.D.SE.SS.LGLSLGGGTILPPA.QS....LSTTPSP.SSLH.DGVEDFRRQLPSQK
Retrocopy MTSHLMGHSQLTTTDESEQSSRLGLSLGGGTILPPA<QSLKHCLSTTPSPISSLHKDGVEDFRRQLPSQK

Parental  TVVEAGKKQKAPKKRKKKDPNEPQKPVSAYALFFRDTQAAIKGQNPNATFGEVSKIVASMWDS-LGEEQK
          TVV....K...P..R....PNE..KPVS..ALFFRDT.A.IKGQNPNA.F..VSKI.ASM.DS.L.....
Retrocopy TVVWKQEKSRRPQRRXXXXPNEAKKPVSSSALFFRDTRAVIKGQNPNASFEGVSKIGASM*DS>LERSKN

Parental  QVYKRKTEAAKKEYLKALAAYKDNQECQATVEAVELDPVPPSQTPSPPPMATVDPASPAPASTEPPALSP
          .....K.....K..LKALA.YKD.QECQATVE..ELDPVPPSQTPSPPPMATVDPASP.PAS.EPPAL.P
Retrocopy RCIRGKPKLPRK-HLKALAEYKDTQECQATVETIELDPVPPSQTPSPPPMATVDPASPPPASAEPPALPP

Parental  SIVVNSTLSSYVANQASSGAGGQPNITKLIITKQMLPSSITMSQGGMVTVIPATVVTSRGIQLGQTSTAT
          SIVVNSTLS.YVANQAS.GAG.QP..TKLIIT.QMLPSS.TMS..GMVT.IPATVV.S.GIQL.QTSTAT
Retrocopy SIVVNSTLSFYVANQASFGAGAQPSVTKLIITRQMLPSSVTMSR-GMVTIIPATVVNSQGIQLSQTSTAT

Parental  IQPSQQAQIVTRSVLQ-AAAAAAASMQLPPPRLQPPPLQQMPQPPTQQQ-VTILQ---QPPP----LQAM
          IQPSQQ.QIVT.SVL...AA........P...L..PP.QQ..Q...QQQ....LQ...QPPP........
Retrocopy IQPSQQTQIVTCSVLE<EAASSTPMTTPPLQQLPQPPTQQ--QVTIQQQ<ASLLQVMPQPPPQKVRINLW

Parental  QQPPPQKVRINLQQQPPP---LQIKIVPP
          QQPP.....I.....PPP....Q...VPP
Retrocopy QQPPALQIKI----APPPTLKMQTTLVPP

Legend:

• *: Stop codon
• >: Forward frameshift by one nucleotide
• <: Reverse frameshift by one nucleotide

Expression

RNA-Seq

Ailuropoda melanoleuca was not studied using RNA-Seq expression data.

ChIP-Seq

Ailuropoda melanoleuca was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_amel_858 retrocopy.

TSS

Ailuropoda melanoleuca was not studied using FANTOM5 data.

Lab

retro_amel_858 was not experimentally validated.

Homology

Retrocopy orthology:

Ailuropoda melanoleuca 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 13 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000006261	1 retrocopy	retro_amel_858 ,
Canis familiaris	ENSCAFG00000005647	2 retrocopies	retro_cfam_1625, retro_cfam_1698,
Choloepus hoffmanni	ENSCHOG00000000714	2 retrocopies	retro_chof_2239, retro_chof_631,
Homo sapiens	ENSG00000092203	1 retrocopy	retro_hsap_2970,
Macropus eugenii	ENSMEUG00000010501	1 retrocopy	retro_meug_1384,
Mustela putorius furo	ENSMPUG00000000181	1 retrocopy	retro_mputfur_718,
Mus musculus	ENSMUSG00000016831	1 retrocopy	retro_mmus_11,
Nomascus leucogenys	ENSNLEG00000014556	1 retrocopy	retro_nleu_2027,
Pongo abelii	ENSPPYG00000005598	1 retrocopy	retro_pabe_2463,
Pan troglodytes	ENSPTRG00000006126	1 retrocopy	retro_ptro_2008,
Sus scrofa	ENSSSCG00000029203	1 retrocopy	retro_sscr_361,