RetrogeneDB ID: retro_amel_937

Retrocopy location

• Organism: Panda (Ailuropoda melanoleuca)
• Coordinates: GL192758.1:1174384..1175050(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSAMEG00000001821
• Aliases: None
• Description: None

Sequence

>retro_amel_937
AAGAAGAAAAATAAGGTTCCTGCTATGCCAGAAACCCTTAAGAAAAAGCAAAGGAATTTCACAGAGTTGAATATCAAGTG
TCTGAGAAAAAAGTTTGCCCAAAAGATGCTTCTAAAGGCAAGGAGAAAGCTTATCTACGAAAAAGCTAAACATTACCACA
AGGAATATAGGCAGATGTACAGAAACTGAGATTTGAATGGCTAGGATGTCAAGAAAAGTTAGCGATTTCTAGGTACCTGC
AGAACCCAAACTGGCATCTGTCATTAGGATGAGAGGTTATCAATGGTCTGAGCCCATAGGCTCGAAAGGTGTTGCAGCTT
CTTCGCCTTCACCAGCTCTTCAATAGCACCTTTGTTAGGTTCAACAAGGCTTCAGTTAACATGCTAAGAACTGTGGGACC
ATATATAGCACGGGGGTACCCAAACCCGATGTTGGTGAATGAACTGATCTACAAAAATGGTTACAACAGAATCAACAAAA
AGCAAATTGCCCTAACATAGAACACATTGATTGCTCAATCTCTTGGTAAATATGGCATCATCTGCATGGAGGATCTGATT
CATGAGGTCTGTACTGTTGGAAAATATTTCAAAGAAGCAAACAACTTTTTATGGCCTTCAAAAATTATCTTCTCCACGAG
GGGGAATGAAGAAAAATGGGGACCAC

Alignment

ORF - retro_amel_937 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 79.46 %
• Parental protein coverage: 85.66 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  EKKKKVPAVPETLKKKRRNFAELKIKRLRKKFAQKMLRKARRKLIYEKAKHYHKEYRQMYR-TEIRMARM
          .KK.KVPA.PETLKKK.RNF.EL.IK.LRKKFAQKML.KARRKLIYEKAKHYHKEYRQMYR.TEI.MARM
Retrocopy KKKNKVPAMPETLKKKQRNFTELNIKCLRKKFAQKMLLKARRKLIYEKAKHYHKEYRQMYR>TEI*MARM

Parental  ARKAGNFDVPAEPKLAFVIRIRG-INGVSPKVRKVLQLLRLRQIFNGTFVKLNKASVNMLRIVEPYIAWG
          .RK...F.VPAEPKLA.VIR.RG.ING.SP..RKVLQLLRL.Q.FN.TFV..NKASVNMLR.V.PYIA.G
Retrocopy SRKVSDF*VPAEPKLASVIRMRG>INGLSP*ARKVLQLLRLHQLFNSTFVRFNKASVNMLRTVGPYIARG

Parental  YPNLKSVNELIYKRGYGKINKKRIALTDNTLIARSLGKYGIICMEDLIHEIYTVGKRFKEANNFLWPF-K
          YPN...VNELIYK.GY..INKK.IALT.NTLIA.SLGKYGIICMEDLIHE..TVGK.FKEANNFLWP..K
Retrocopy YPNPMLVNELIYKNGYNRINKKQIALT*NTLIAQSLGKYGIICMEDLIHEVCTVGKYFKEANNFLWPS>K

Parental  LSSPRGGMKKKTTH
          LSSPRGGMKK...H
Retrocopy LSSPRGGMKKNGDH

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_937 retrocopy.

TSS

Ailuropoda melanoleuca was not studied using FANTOM5 data.

Lab

retro_amel_937 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 9 parental genes, and 73 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000001821	5 retrocopies	retro_amel_1230, retro_amel_1632, retro_amel_760, retro_amel_933, retro_amel_937 ,
Ailuropoda melanoleuca	ENSAMEG00000012791	2 retrocopies	retro_amel_1260, retro_amel_243,
Canis familiaris	ENSCAFG00000008021	28 retrocopies	retro_cfam_1039, retro_cfam_1075, retro_cfam_1079, retro_cfam_1167, retro_cfam_1209, retro_cfam_1236, retro_cfam_1270, retro_cfam_1308, retro_cfam_1390, retro_cfam_1436, retro_cfam_1445, retro_cfam_1453, retro_cfam_1524, retro_cfam_1541, retro_cfam_1699, retro_cfam_1755, retro_cfam_1855, retro_cfam_1856, retro_cfam_2051, retro_cfam_2192, retro_cfam_338, retro_cfam_403, retro_cfam_563, retro_cfam_609, retro_cfam_737, retro_cfam_74, retro_cfam_922, retro_cfam_998,
Dasypus novemcinctus	ENSDNOG00000017654	15 retrocopies	retro_dnov_1561, retro_dnov_1692, retro_dnov_182, retro_dnov_1893, retro_dnov_209, retro_dnov_2158, retro_dnov_2568, retro_dnov_264, retro_dnov_2657, retro_dnov_279, retro_dnov_287, retro_dnov_365, retro_dnov_655, retro_dnov_77, retro_dnov_971,
Felis catus	ENSFCAG00000028446	6 retrocopies	retro_fcat_1643, retro_fcat_230, retro_fcat_255, retro_fcat_338, retro_fcat_342, retro_fcat_945,
Latimeria chalumnae	ENSLACG00000003571	1 retrocopy	retro_lcha_63,
Macropus eugenii	ENSMEUG00000016319	9 retrocopies	retro_meug_1002, retro_meug_1449, retro_meug_1942, retro_meug_1947, retro_meug_60, retro_meug_760, retro_meug_84, retro_meug_968, retro_meug_99,
Monodelphis domestica	ENSMODG00000007136	4 retrocopies	retro_mdom_1341, retro_mdom_1998, retro_mdom_371, retro_mdom_66,
Sus scrofa	ENSSSCG00000006182	3 retrocopies	retro_sscr_1138, retro_sscr_209, retro_sscr_796,