RetrogeneDB ID: retro_amel_1227

Retrocopy location

• Organism: Panda (Ailuropoda melanoleuca)
• Coordinates: GL193068.1:921282..922248(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSAMEG00000007786
• Aliases: None
• Description: Elongation factor 1-alpha [Source:UniProtKB/TrEMBL;Acc:G1LMH6]

Sequence

>retro_amel_1227
TTGGGCTACACACTGGGTGTGAAACAACTAATTGTTGGTGTTAACAAAATGGATTCCTCTGAGCCACCCTATGGCCAGAA
GAGATACAGGAAATCATTACAGAAGTCAGCACCTACAATAAGAAAATTGGGTACAACCCCGACATGTTAGCATTTGTGCC
AATTTCTGGTTGAAATGGTGACAACAGTCTGGAGCCAAGTGCTAAGTCTTGGTTCAACGGATGGAAAGTCACCCGTAAAG
ATGACAATACCAGTGGAACCACACTGTTTAAAGCTCTGGATGACATTCTGCCATCAACTCATCCAACTGACAAACCCTTG
CATCTTCCCCTAGAGGATGCCTACAAAATTGGTGGTATTGGTACTGTCCCTGTGGGCCAAGTGGAGACTGTTGTTCTTAA
ACCTAGCTTGTGGTCACCTTTGCTCTAGTCAATGTTACATCTGAAGTAAAGTCTGTTGAAATGCACCATGAAGCTTTGAG
TTAGGCTCTTCCTGGGGACAAAGTGGGCTTCAATGTCAAGAACATATCTGTCAAAGATGTTCGTAGTGACACTGAAGCTA
GTGACAGCAAAAATGACCCACCAATGGAAGCAGCTGGCTTCACAGCTCAGGTGATTATCCTGAACCATCCAGGCCAAATC
AGTGCTGGATATGCACCTGTGCTGGATTGTCACACAGTTCACATTTCTTGCAAGTTTGCTGAGCTAAAGGAGAAGATTGA
TTGTTGTTCTGGAAAAAAGCTGGAAAGTGGTCCCAAGTTCTTGAAATCTGGTGATGCTGCCATCATCGATATGGTTCTTG
GCAAGCCTGTGTGTGTTGAGAGCTTCTCTGACTATCCTCCTCTGGGTTGTTTTGCTGTTCGTGACATGAGACAGACAGCT
GCTGTGGCTGTCATCAAAGCAGTGGCCAAGAAAGCAGCTGGAGCTGGTAAGGTCACAAGTCTTCCCAGAAAGCTCAGGAG
GCTAAA

Alignment

ORF - retro_amel_1227 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 82.87 %
• Parental protein coverage: 69.08 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  LAYTLGVKQLIVGVNKMDSTEPPYSQKRY-EEIVKEVSTYIKKIGYNPDTVAFVPISGWNGDNMLEPSAN
          L.YTLGVKQLIVGVNKMDS.EPPY.QKRY..EI..EVSTY.KKIGYNPD..AFVPISG.NGDN.LEPSA.
Retrocopy LGYTLGVKQLIVGVNKMDSSEPPYGQKRY<QEIITEVSTYNKKIGYNPDMLAFVPISG*NGDNSLEPSAK

Parental  MPWFKGWKVTRKDGNASGTTLLEALDCILPPTRPTDKPLRLPLQDVYKIGGIGTVPVGRVETGVLKPGM-
          ..WF.GWKVTRKD.N.SGTTL..ALD.ILP.T.PTDKPL.LPL.D.YKIGGIGTVPVG.VET.VLKP...
Retrocopy S-WFNGWKVTRKDDNTSGTTLFKALDDILPSTHPTDKPLHLPLEDAYKIGGIGTVPVGQVETVVLKPSL<

Parental  VVTFAPVNVTTEVKSVEMHHEALSEALPGDNVGFNVKNVSVKDVRRGNVAGDSKNDPPMEAAGFTAQVII
          VVTFA.VNVT.EVKSVEMHHEALS.ALPGD.VGFNVKN.SVKDVR....A.DSKNDPPMEAAGFTAQVII
Retrocopy VVTFALVNVTSEVKSVEMHHEALS*ALPGDKVGFNVKNISVKDVRSDTEASDSKNDPPMEAAGFTAQVII

Parental  LNHPGQISAGYAPVLDCHTAHIACKFAELKEKIDRRSGKKLEDGPKFLKSGDAAIVDMVPGKPMCVESFS
          LNHPGQISAGYAPVLDCHT.HI.CKFAELKEKID..SGKKLE.GPKFLKSGDAAI.DMV.GKP.CVESFS
Retrocopy LNHPGQISAGYAPVLDCHTVHISCKFAELKEKIDCCSGKKLESGPKFLKSGDAAIIDMVLGKPVCVESFS

Parental  DYPPLGRFAVRDMRQTVAVGVIKAVDKKAAGAGKVT-KSAQKAQKAK
          DYPPLG.FAVRDMRQT.AV.VIKAV.KKAAGAGKVT.KS.QKAQ.AK
Retrocopy DYPPLGCFAVRDMRQTAAVAVIKAVAKKAAGAGKVT<KSSQKAQEAK

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_1227 retrocopy.

TSS

Ailuropoda melanoleuca was not studied using FANTOM5 data.

Lab

retro_amel_1227 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 10 parental genes, and 45 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000007786	14 retrocopies	retro_amel_1064, retro_amel_1072, retro_amel_1079, retro_amel_1140, retro_amel_1167, retro_amel_1203, retro_amel_1227 , retro_amel_1283, retro_amel_1371, retro_amel_160, retro_amel_1742, retro_amel_1797, retro_amel_1855, retro_amel_200,
Canis familiaris	ENSCAFG00000013249	1 retrocopy	retro_cfam_1007,
Dipodomys ordii	ENSDORG00000009629	1 retrocopy	retro_dord_509,
Equus caballus	ENSECAG00000022260	1 retrocopy	retro_ecab_802,
Erinaceus europaeus	ENSEEUG00000000342	3 retrocopies	retro_eeur_407, retro_eeur_492, retro_eeur_625,
Loxodonta africana	ENSLAFG00000028081	1 retrocopy	retro_lafr_651,
Monodelphis domestica	ENSMODG00000018533	4 retrocopies	retro_mdom_1053, retro_mdom_1146, retro_mdom_311, retro_mdom_792,
Mus musculus	ENSMUSG00000037742	15 retrocopies	retro_mmus_1349, retro_mmus_1518, retro_mmus_1667, retro_mmus_1783, retro_mmus_1816, retro_mmus_1849, retro_mmus_1850, retro_mmus_1864, retro_mmus_1909, retro_mmus_2363, retro_mmus_2583, retro_mmus_2902, retro_mmus_3249, retro_mmus_480, retro_mmus_483,
Ictidomys tridecemlineatus	ENSSTOG00000007687	4 retrocopies	retro_itri_1509, retro_itri_1740, retro_itri_1816, retro_itri_195,
Drosophila melanogaster	FBgn0000557	1 retrocopy	retro_dmel_9,