RetrogeneDB ID: retro_amel_1412

Retrocopy location

• Organism: Panda (Ailuropoda melanoleuca)
• Coordinates: GL193341.1:110309..111294(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: CNN3
• Ensembl ID: ENSAMEG00000016707
• Aliases: None
• Description: calponin 3, acidic [Source:HGNC Symbol;Acc:2157]

Sequence

>retro_amel_1412
ATGACCCACTTCAGCTAGGGCCCTTCTTAACAGGCTCTCCATCGAGGTCAAGAGCAAGATCACTTCTAAGCATGAGCATC
AGGCAGAAGATCTTCAAAACTGGACAGAAGAGGAGACAGGCATGAGCACTGGCATCAACTTTCAGTTGGGCTTAAAAGAT
GGCATCATCCTCTGCGAGCTCATAAACAAGCTACAGCCAGGATCAGTGAAGAAGGTTAATGACTCCTCGTTAAACTGGCC
TCAGCTGGAGAATACTGGCAACTTTATTAAAGCTATTCAGGCCTACGGCATGAAGCCACATGACATATTTGAAGCAAATG
ATCTTTTTGAGAACAGAAATGTGACCCAGGTTCAGACTATGCTGGTGGCTCTGGCAGGTCTGGCTAAAACAAAAGGATTC
CATACAACCACTGACACTGGAGTTAAGTATGATGAAAAACAAACAAGGCGTTTTGACGAAGGAAAATTAAAAGCTGGCCG
AAGTGTAATTGGTTTGCAGGTGTGAACCAACAAATGCGCCAGCCAGGCAGGTATGGCAGCCGATGGGACCAGGAGGCATC
TTTATGATCCCAAAATGCAAACTGACAAACCTTTTGACCAGACCACAATTAGTCTGCAGATGGGCAAAAACAAAGGAGCC
AGCCAGGCAGAGATGTTCGCACCAGGTACCAGAAGAGACATCTATGGTCAGAAGGTAACATTACAACCAGTGGACAACTC
AACAATTTCTCTACAGATGGGAACCAACAAAGTTGCTTCCCAGAAAGGAATGAGTGTGTATGGGCTTGGGCGGCAAGTAC
ACGATCCCAAATACTGTGCCGCTACCACAGAACTTGTAATTCACAATGGAAGCCAAGGAACAGGAACAAATGGGTCTGAA
ATTAGCGATAGTGATTATCAGGCAGAATACCCAGATGAATATCATGGAGAGTACCCAGATGACCACCCCAGAGATTACCA
ATATGGCGACCAAGGCACTGATTAT

Alignment

ORF - retro_amel_1412 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 88.18 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MTHFNKGPS-YGLSAEVKNKIASKYDHQAEEDLRNWIEEVTGMSIGTNFQLGLKDGIILCELINKLQPGS
          MTHF..GPS...LS.EVK.KI.SK..HQAE.DL.NW.EE.TGMS.G.NFQLGLKDGIILCELINKLQPGS
Retrocopy MTHFS*GPS>NRLSIEVKSKITSKHEHQAE-DLQNWTEEETGMSTGINFQLGLKDGIILCELINKLQPGS

Parental  VKKVNESSLNWPQLENIGNFIKAIQAYGMKPHDIFEANDLFENGNMTQVQTTLVALAGLAKTKGFHTTID
          VKKVN.SSLNWPQLEN.GNFIKAIQAYGMKPHDIFEANDLFEN.N.TQVQT.LVALAGLAKTKGFHTT.D
Retrocopy VKKVNDSSLNWPQLENTGNFIKAIQAYGMKPHDIFEANDLFENRNVTQVQTMLVALAGLAKTKGFHTTTD

Parental  IGVKYAEKQTRRFDEGKLKAGQSVIGLQMGTNKCASQAGMTAYGTRRHLYDPKMQTDKPFDQTTISLQMG
          .GVKY.EKQTRRFDEGKLKAG.SVIGLQ..TNKCASQAGM.A.GTRRHLYDPKMQTDKPFDQTTISLQMG
Retrocopy TGVKYDEKQTRRFDEGKLKAGRSVIGLQV*TNKCASQAGMAADGTRRHLYDPKMQTDKPFDQTTISLQMG

Parental  TNKGASQAGMLAPGTRRDIYDQKLTLQPVDNSTISLQMGTNKVASQKGMSVYGLGRQVYDPKYCAAPTEP
          .NKGASQA.M.APGTRRDIY.QK.TLQPVDNSTISLQMGTNKVASQKGMSVYGLGRQV.DPKYCAA.TE.
Retrocopy KNKGASQAEMFAPGTRRDIYGQKVTLQPVDNSTISLQMGTNKVASQKGMSVYGLGRQVHDPKYCAATTEL

Parental  VIHNGSQGTGTNGSEISDSDYQAEYPDEYHGEYPDDYPRDYQYGDQGVDY
          VIHNGSQGTGTNGSEISDSDYQAEYPDEYHGEYPDD.PRDYQYGDQG.DY
Retrocopy VIHNGSQGTGTNGSEISDSDYQAEYPDEYHGEYPDDHPRDYQYGDQGTDY

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_1412 retrocopy.

TSS

Ailuropoda melanoleuca was not studied using FANTOM5 data.

Lab

retro_amel_1412 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 14 parental genes, and 19 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000000062	1 retrocopy	retro_amel_675,
Ailuropoda melanoleuca	ENSAMEG00000016707	1 retrocopy	retro_amel_1412 ,
Ailuropoda melanoleuca	ENSAMEG00000018148	1 retrocopy	retro_amel_1893,
Bos taurus	ENSBTAG00000020345	1 retrocopy	retro_btau_1211,
Callithrix jacchus	ENSCJAG00000018128	3 retrocopies	retro_cjac_1331, retro_cjac_533, retro_cjac_861,
Echinops telfairi	ENSETEG00000010095	1 retrocopy	retro_etel_638,
Homo sapiens	ENSG00000117519	1 retrocopy	retro_hsap_3419,
Gorilla gorilla	ENSGGOG00000013870	1 retrocopy	retro_ggor_2312,
Macropus eugenii	ENSMEUG00000002921	2 retrocopies	retro_meug_2020, retro_meug_42,
Macaca mulatta	ENSMMUG00000001690	1 retrocopy	retro_mmul_1747,
Monodelphis domestica	ENSMODG00000004326	1 retrocopy	retro_mdom_442,
Mus musculus	ENSMUSG00000053931	2 retrocopies	retro_mmus_1052, retro_mmus_2544,
Sarcophilus harrisii	ENSSHAG00000002670	1 retrocopy	retro_shar_567,
Vicugna pacos	ENSVPAG00000004889	2 retrocopies	retro_vpac_190, retro_vpac_449,