RetrogeneDB ID: retro_amel_1752

Retrocopy location

• Organism: Panda (Ailuropoda melanoleuca)
• Coordinates: GL194205.1:15794..16778(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: KIAA0020
• Ensembl ID: ENSAMEG00000012187
• Aliases: None
• Description: KIAA0020 [Source:HGNC Symbol;Acc:29676]

Sequence

>retro_amel_1752
AAGATCATAGGAAAAGGTGCAAAGACATCACAAGAAAAAAACAGATTTCATAAAAACAATGATTCTGGTTCATTGAAGAC
ATTTCCAAGAAAAGTTATCAAGGAAGGTGGCCCTAAAATCACATCGAATAACTTTGAGAAATGTGCCACAAAACCTGGGA
AAAAAGGTGTAAAACAGTTTAAAAATAAGCAGCAAGGGGATAAAATACCAAAGAACAAATTCCAGCAACCAAATCAGCAG
GAAAAGAAAATTCCAGGCAGACCGTAAATGTGATGAATCAGCAGCCAAGACACCTAAGTGGGATGACTTCGAAAAGAAGA
AAGAACTAAAGCAAAGCATGCAACTTGGTGATAAAACCAACTATGACGTTGTTCTGGCAAAGCAGATTTGGGAGATCTTA
AGAAGAAAAGACTGTGACAAAGAAAAGAGAGTGAAGTTGATAAGTGATTTGCAGAAGCTGATTCAAGGGAAAATTAAAAT
TATCACATTTGCCCATGAGTCAACTTGTATGATCCAGTATTACATTCAGTGTGGTAATGAAGAACAGCAAAAACAGGCTT
TTGAAGAACTGCAAGATGATTTGGTCCAATTAAGTAAAGCTAAATATTCCAGAGCTATTAAGAAATTTTTCATGTATGGG
AGTAAGCCACAGATTGCAGAGATAATGAGAAGTTTTAAAGGCCATGTGAGGAAGATGCTCTGGCATGCAGAAGTGTCCAC
AATTGTGGAATATGTGTACAATGACGAAGCCATCTTGGAGGAGAGGAACATGCTGAGGGACGAGCTCTATGAGAACACAT
TTCAGCTTTACAAGTCAGCTGATCACCCAACTCTGGATAAAGTATTAGAGGTATAGCCAGGAAAAACAGAGCTTATCATG
GATGAAATGAAGCAGATTCTAACTCCAATGGCCCAAAAGGAAGCTGTGATTAAGTACTCATTGGTCATATAGTATTCTTG
GACTTTTAAACCCATGCACCCCCA

Alignment

ORF - retro_amel_1752 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 79.1 %
• Parental protein coverage: 51.47 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  KFTGKGAKTSQEKNRFHKNNDSGSSKTFPRRVGKEGGPKITSKNFEKCATKPGKKGVKQF-KNKQQGDKI
          K..GKGAKTSQEKNRFHKNNDSGS.KTFPR.V.KEGGPKITS.NFEKCATKPGKKGVKQF.K....G.K.
Retrocopy KIIGKGAKTSQEKNRFHKNNDSGSLKTFPRKVIKEGGPKITSNNFEKCATKPGKKGVKQF>KISSKGIKY

Parental  PKNKFQQANKFNKKRKFQADGKSDESAAKKPKWDDFKKKKKELKQSRQLSDKTNYDIVVRAKQIWESLRR
          ........N....KRKFQAD.K.DESAAK.PKWDDF.KKK.ELKQS.QL.DKTNYD.V..AKQIWE.LRR
Retrocopy QRTN--SSNQISRKRKFQADRKCDESAAKTPKWDDFEKKK-ELKQSMQLGDKTNYDVVL-AKQIWEILRR

Parental  KDCDKEKRVKLMGDLQKLIQGKIKTMAFAHDSTRVIQCYIQFGNEEQRKQAFEELRDDLVQLSKAKYSRN
          KDCDKEKRVKL..DLQKLIQGKIK...FAH.ST..IQ.YIQ.GNEEQ.KQAFEEL.DDLVQLSKAKYSR.
Retrocopy KDCDKEKRVKLISDLQKLIQGKIKIITFAHESTCMIQYYIQCGNEEQQKQAFEELQDDLVQLSKAKYSRA

Parental  IVKKFLMYGSKAQIAEIMRSFKGHVRKMLRHAEASAVVEYAYNDKAILEQRNMLAEELYGNTFQLYKSAD
          I.KKF.MYGSK.QIAEIMRSFKGHVRKML.HAE.S..VEY.YND.AILE.RNML..ELY.NTFQLYKSAD
Retrocopy I-KKFFMYGSKPQIAEIMRSFKGHVRKMLWHAEVSTIVEYVYNDEAILEERNMLRDELYENTFQLYKSAD

Parental  HPTLDKVLEVQPEKLELIMDEMKQILTPMAQKEAVIKHSLV-HKVFLDFFTYAPP
          HPTLDKVLEV.P.K.ELIMDEMKQILTPMAQKEAVIK.SLV.H.VFLDF.T.APP
Retrocopy HPTLDKVLEV*PGKTELIMDEMKQILTPMAQKEAVIKYSLV<HIVFLDF*THAPP

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_1752 retrocopy.

TSS

Ailuropoda melanoleuca was not studied using FANTOM5 data.

Lab

retro_amel_1752 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.

---

Parental genes homology:

Parental genes homology involve 7 parental genes, and 7 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000012187	1 retrocopy	retro_amel_1752 ,
Callithrix jacchus	ENSCJAG00000010917	1 retrocopy	retro_cjac_2253,
Cavia porcellus	ENSCPOG00000008552	1 retrocopy	retro_cpor_1158,
Loxodonta africana	ENSLAFG00000017341	1 retrocopy	retro_lafr_1029,
Mus musculus	ENSMUSG00000041360	1 retrocopy	retro_mmus_3640,
Oryctolagus cuniculus	ENSOCUG00000004189	1 retrocopy	retro_ocun_213,
Sorex araneus	ENSSARG00000000579	1 retrocopy	retro_sara_499,